Getting started
The tools for your .cools
Chromosome conformation capture technologies reveal the incredible complexity of genome folding. A growing number of labs and multiple consortia, including the 4D Nucleome, the International Nucleome Consortium, and ENCODE, are generating higher-resolution datasets to probe genome architecture across cell states, types, and organisms. Larger datasets increase the challenges at each step of computational analysis, from storage, to memory, to researchers’ time. The recently-introduced cooler format readily handles storage of high-resolution datasets via a sparse data model.
cooltools leverages this format to enable flexible and reproducible analysis of high-resolution data. cooltools provides a suite of computational tools with a paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation.
If you use cooltools in your work, please cite cooltools: https://doi.org/10.1101/2022.10.31.514564.
Installation
Requirements
Python 3.7+
Scientific Python packages
Install using pip
Compile and install cooltools and its Python dependencies from PyPI using pip:
$ pip install cooltools
or install the latest version directly from github:
$ pip install https://github.com/open2c/cooltools/archive/refs/heads/master.zip
Install the development version
Finally, you can install the latest development version of cooltools from github. First, make a local clone of the github repository:
$ git clone https://github.com/open2c/cooltools
Then, you can compile and install cooltools in development mode, which installs the package without moving it to a system folder and thus allows immediate live-testing any changes in the python code.
$ cd cooltools
$ pip install -e ./
Visualization
Welcome to the cooltools visualization notebook!
Visualization is a crucial part of analyzing large-scale datasets. Before performing analyses of new Hi-C datasets, it is highly recommend to visualize the data. This notebook contains tips and tricks for visualization of coolers using cooltools.
Current topics:
Smoothing, interpolation, and adaptive coarsegraining
Future topics:
higlass-python
translocations, structural variants
visualizing matrices for other organisms
[1]:
# import standard python libraries
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import os
[2]:
# download test data
# this file is 145 Mb, and may take a few seconds to download
import cooltools
data_dir = './data/'
cool_file = cooltools.download_data("HFF_MicroC", cache=True, data_dir=data_dir)
print(cool_file)
./data/test.mcool
[3]:
#import python package for working with cooler files: https://github.com/open2c/cooler
import cooler
Inspecting C data
The file we just downloaded, test.mcool, contains Micro-C data from HFF cells for two chromosomes in a multi-resolution mcool format.
[4]:
# to print which resolutions are stored in the mcool, use list_coolers
cooler.fileops.list_coolers(f'{data_dir}/test.mcool')
[4]:
['/resolutions/1000',
'/resolutions/10000',
'/resolutions/100000',
'/resolutions/1000000']
[5]:
### to load a cooler with a specific resolution use the following syntax:
clr = cooler.Cooler(f'{data_dir}/test.mcool::resolutions/1000000')
### to print chromosomes and binsize for this cooler
print(f'chromosomes: {clr.chromnames}, binsize: {clr.binsize}')
### to make a list of chromosome start/ends in bins:
chromstarts = []
for i in clr.chromnames:
print(f'{i} : {clr.extent(i)}')
chromstarts.append(clr.extent(i)[0])
chromosomes: ['chr2', 'chr17'], binsize: 1000000
chr2 : (0, 243)
chr17 : (243, 327)
Coolers store pairwise contact frequencies in sparse format, which can be fetched on demand as dense matrices. clr.matrix returns a matrix selector. The selector supports Python slice syntax [] and a .fetch() method. Slicing clr.matrix() with [:] fetches all bins in the cooler. Fetching can return either balanced, or corrected, contact frequences (balance=True), or raw counts prior to bias removal (balance=False).
In genome-wide C data for mammalian cells in interphase, the following features are typically observed:
Higher contact frequencies within a chromosome as opposed to between chromosomes; this is consistent with observations of chromosome territories. See below.
More frequent contacts between regions at shorter genomic separations. Characterizing this is explored in more detail in the contacts_vs_dist notebook.
A plaid pattern of interactions, termed compartments. Characterizing this is explored in more detail in the compartments notebook.
Each of these features are visible below.
Visualizing C data
Plotting raw counts
First, we plot raw counts with a linear colormap thresholded at 500 counts for the entire cooler. Note that the number of counts per cooler depends on the sequencing depth of the experiment, and a different threshold may be needed to see the same features.
[6]:
f, ax = plt.subplots(
figsize=(7,6))
im = ax.matshow((clr.matrix(balance=False)[:]),vmax=500);
plt.colorbar(im ,fraction=0.046, pad=0.04, label='raw counts')
ax.set(xticks=chromstarts, xticklabels=clr.chromnames,
xlabel='position, chrom#', ylabel='position, bin#')
ax.xaxis.set_label_position('top')
Plotting subregions
Below, we fetch and plot an individual chromosome (left) and a region of a chromosome (right) using clr.fetch()
[7]:
# to plot ticks in terms of megabases we use the EngFormatter
# https://matplotlib.org/gallery/api/engineering_formatter.html
from matplotlib.ticker import EngFormatter
bp_formatter = EngFormatter('b')
def format_ticks(ax, x=True, y=True, rotate=True):
if y:
ax.yaxis.set_major_formatter(bp_formatter)
if x:
ax.xaxis.set_major_formatter(bp_formatter)
ax.xaxis.tick_bottom()
if rotate:
ax.tick_params(axis='x',rotation=45)
f, axs = plt.subplots(
figsize=(14,4),
ncols=3)
ax = axs[0]
im = ax.matshow(clr.matrix(balance=False)[:], vmax=2500);
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='raw counts');
ax.set_xticks(chromstarts)
ax.set_xticklabels(clr.chromnames)
ax.set_yticks(chromstarts)
ax.set_yticklabels(clr.chromnames)
ax.xaxis.tick_bottom()
ax.set_title('All data')
ax = axs[1]
im = ax.matshow(
clr.matrix(balance=False).fetch('chr17'),
vmax=2500,
extent=(0,clr.chromsizes['chr17'], clr.chromsizes['chr17'], 0)
);
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='raw counts');
ax.set_title('chr17', y=1.08)
ax.set_ylabel('position, Mb')
format_ticks(ax)
ax = axs[2]
start, end = 30_000_000, 60_000_000
region = ('chr17', start, end)
im = ax.matshow(
clr.matrix(balance=False).fetch(region),
vmax=2500,
extent=(start, end, end, start)
);
ax.set_title(f'chr17:{start:,}-{end:,}', y=1.08)
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='raw counts');
format_ticks(ax)
plt.tight_layout()
Logarithmic color scale
Since C data has a high dynamic range, we often plot the data in log-scale. This enables simultaneous visualization of features near and far from the diagonal in a consistent colorscale. Note that regions with no reported counts are evident as white stripes at both centromeres. This occurs because reads are not uniquely mapped to these highly-repetitive regions. These regions are masked before matrix balancing.
[8]:
# plot heatmaps at megabase resolution with 3 levels of zoom in log-scale with a consistent colormap#
from matplotlib.colors import LogNorm
f, axs = plt.subplots(
figsize=(14,4),
ncols=3)
bp_formatter = EngFormatter('b')
norm = LogNorm(vmax=50_000)
ax = axs[0]
im = ax.matshow(
clr.matrix(balance=False)[:],
norm=norm,
)
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='raw counts');
ax.set_xticks(chromstarts)
ax.set_xticklabels(clr.chromnames)
ax.set_yticks(chromstarts)
ax.set_yticklabels(clr.chromnames)
ax.xaxis.tick_bottom()
ax.set_title('All data')
ax = axs[1]
im = ax.matshow(
clr.matrix(balance=False).fetch('chr17'),
norm=norm,
extent=(0,clr.chromsizes['chr17'], clr.chromsizes['chr17'], 0)
);
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='raw counts');
ax.set_title('chr17', y=1.08)
ax.set(ylabel='position, Mb', xlabel='position, Mb')
format_ticks(ax)
ax = axs[2]
start, end = 30_000_000, 60_000_000
region = ('chr17', start, end)
im = ax.matshow(
clr.matrix(balance=False).fetch(region),
norm=norm,
extent=(start, end, end, start)
);
ax.set_title(f'chr17:{start:,}-{end:,}', y=1.08)
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='raw counts');
ax.set(xlabel='position, Mb')
format_ticks(ax)
plt.tight_layout()
Colormaps
cooltools.lib.plotting registers a set of colormaps that are useful for visualizing C data. In particular, the fall colormap (inspired by colorbrewer) offers a high dynamic range, linear, option for visualizing Hi-C matrices. This often displays features more clearly than red colormaps.
[9]:
### plot the corrected data in fall heatmap and compare to the white-red colormap ###
### thanks for the alternative collormap naming to https://twitter.com/HiC_memes/status/1286326919122825221/photo/1###
import cooltools.lib.plotting
vmax = 5000
norm = LogNorm(vmin=1, vmax=100_000)
fruitpunch = sns.blend_palette(['white', 'red'], as_cmap=True)
f, axs = plt.subplots(
figsize=(13, 10),
nrows=2,
ncols=2,
sharex=True, sharey=True)
ax = axs[0, 0]
ax.set_title('Pumpkin Spice')
im = ax.matshow(clr.matrix(balance=False)[:], vmax=vmax, cmap='fall');
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='counts (linear)');
plt.xticks(chromstarts,clr.chromnames);
ax = axs[0, 1]
ax.set_title('Fruit Punch')
im3 = ax.matshow(clr.matrix(balance=False)[:], vmax=vmax, cmap=fruitpunch);
plt.colorbar(im3, ax=ax, fraction=0.046, pad=0.04, label='counts (linear)');
plt.xticks(chromstarts,clr.chromnames);
ax = axs[1, 0]
im = ax.matshow(clr.matrix(balance=False)[:], norm=norm, cmap='fall');
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='counts (log)');
plt.xticks(chromstarts,clr.chromnames);
ax = axs[1, 1]
im3 = ax.matshow(clr.matrix(balance=False)[:], norm=norm, cmap=fruitpunch);
plt.colorbar(im3, ax=ax, fraction=0.046, pad=0.04, label='counts (log)');
plt.xticks(chromstarts,clr.chromnames);
plt.tight_layout()
The utility of fall colormaps becomes more noticeable at higher resolutions and higher degrees of zoom.
[10]:
### plot the corrected data in fall heatmap ###
import cooltools.lib.plotting
clr_10kb = cooler.Cooler(f'{data_dir}/test.mcool::resolutions/10000')
region = 'chr17:30,000,000-35,000,000'
extents = (start, end, end, start)
norm = LogNorm(vmin=1, vmax=1000)
f, axs = plt.subplots(
figsize=(13, 10),
nrows=2,
ncols=2,
sharex=True,
sharey=True
)
ax = axs[0, 0]
im = ax.matshow(
clr_10kb.matrix(balance=False).fetch(region),
cmap='fall',
vmax=200,
extent=extents
);
plt.colorbar(im, ax=ax ,fraction=0.046, pad=0.04, label='counts');
ax = axs[0, 1]
im2 = ax.matshow(
clr_10kb.matrix(balance=False).fetch(region),
cmap=fruitpunch,
vmax=200,
extent=extents
);
plt.colorbar(im2, ax=ax, fraction=0.046, pad=0.04, label='counts');
ax = axs[1, 0]
im = ax.matshow(
clr_10kb.matrix(balance=False).fetch(region),
cmap='fall',
norm=norm,
extent=extents
);
plt.colorbar(im, ax=ax, fraction=0.046, pad=0.04, label='counts');
ax = axs[1, 1]
im2 = ax.matshow(
clr_10kb.matrix(balance=False).fetch(region),
cmap=fruitpunch,
norm=norm,
extent=extents
);
plt.colorbar(im2, ax=ax, fraction=0.046, pad=0.04, label='counts');
for ax in axs.ravel():
format_ticks(ax, rotate=False)
plt.tight_layout()
Balancing
When (balance=True) is passed to cooler.matrix(), this applies correction weights calculated from matrix balancing. Matrix balancing (also called iterative correction and KR normalization) removes multiplicative biases, which constitute the majority of known biases, from C data. By default, the rows & columns of the matrix are normalized to sum to one (note that the colormap scale differs after balancing). Biases, also called weights for normalization, are stored in the weight column of
the bin table given by clr.bins().
[11]:
clr.bins()[:3]
[11]:
| chrom | start | end | weight | |
|---|---|---|---|---|
| 0 | chr2 | 0 | 1000000 | 0.002441 |
| 1 | chr2 | 1000000 | 2000000 | 0.002435 |
| 2 | chr2 | 2000000 | 3000000 | 0.002728 |
Before balancing, cooler also applies filters to remove low-coverage bins (note that peri-centromeric bins are completely removed in the normalized data). Filtered bins are stored as np.nan in the weights.
Matrices appear visually smoother after removal of biases. Smoother matrices are expected for chromosomes, as adjacent regions along a chromosome are connected and should only slowly vary in their contact frequencies with other regions.
[12]:
### plot the raw and corrected data in logscale ###
from mpl_toolkits.axes_grid1 import make_axes_locatable
plt_width=4
f, axs = plt.subplots(
figsize=( plt_width+plt_width+2, plt_width+plt_width+1),
ncols=4,
nrows=3,
gridspec_kw={'height_ratios':[4,4,1],"wspace":0.01,'width_ratios':[1,.05,1,.05]},
constrained_layout=True
)
norm = LogNorm(vmax=0.1)
norm_raw = LogNorm(vmin=1, vmax=10_000)
ax = axs[0,0]
im = ax.matshow(
clr.matrix(balance=False)[:],
norm=norm_raw,
cmap='fall',
aspect='auto'
);
ax.xaxis.set_visible(False)
ax.set_title('full matrix')
ax.set_ylabel('raw', fontsize=16)
cax = axs[0,1]
plt.colorbar(im, cax=cax, label='raw counts')
ax = axs[1,0]
im = ax.matshow(
clr.matrix()[:],
norm=norm,
cmap='fall',
);
ax.xaxis.set_visible(False)
ax.set_ylabel('balanced', fontsize=16)
cax = axs[1,1]
plt.colorbar(im, cax=cax, label='corrected freqs')
ax1 = axs[2,0]
weights = clr.bins()[:]['weight'].values
ax1.plot(weights)
ax1.set_xlim([0, len(clr.bins()[:])])
ax1.set_xlabel('position, bins')
ax1 = axs[2,1]
ax1.set_visible(False)
start = 30_000_000
end = 32_000_000
region = ('chr17', start, end)
ax = axs[0,2]
im = ax.matshow(
clr_10kb.matrix(balance=False).fetch(region),
norm=norm_raw,
cmap='fall'
);
ax.set_title(f'chr17:{start:,}-{end:,}')
ax.xaxis.set_visible(False)
cax = axs[0,3]
plt.colorbar(im, cax=cax, label='raw counts');
ax = axs[1,2]
im = ax.matshow(
clr_10kb.matrix().fetch(region),
norm=norm,
cmap='fall',
extent=(start, end, end, start)
);
ax.xaxis.set_visible(False)
cax = axs[1,3]
plt.colorbar(im, cax=cax, label='corrected frequencies');
ax1 = axs[2,2]
weights = clr_10kb.bins().fetch(region)['weight'].values
ax1.plot(
np.linspace(start, end, len(weights)),
weights
)
format_ticks(ax1, y=False, rotate=False)
ax1.set_xlim(start, end);
ax1.set_xlabel('chr17 position, bp')
ax1 = axs[2,3]
ax1.set_visible(False)
Coverage
Contact matrices often display varible tendency to make contacts within versus between chromosomes. This can be calculated in cooltools with cooltools.coverage and is often plotted as a ratio of (cis_coverage/total_coverage). Note that the total coverge is similar to, but distinct from, the iteratively calculated balancing weights (see above).
[13]:
cis_coverage, tot_coverage = cooltools.coverage(clr)
f, ax = plt.subplots(
figsize=(15, 10),
)
norm = LogNorm(vmax=0.1)
im = ax.matshow(
clr.matrix()[:],
norm=norm,
cmap='fall'
);
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.1)
plt.colorbar(im, cax=cax, label='corrected frequencies');
ax.set_title('full matrix')
ax.xaxis.set_visible(False)
ax1 = divider.append_axes("bottom", size="25%", pad=0.1, sharex=ax)
weights = clr.bins()[:]['weight'].values
ax1.plot( cis_coverage, label='cis')
ax1.plot( tot_coverage, label='total')
ax1.set_xlim([0, len(clr.bins()[:])])
ax1.set_ylabel('Coverage')
ax1.legend()
ax1.set_xticks([])
ax2 = divider.append_axes("bottom", size="25%", pad=0.1, sharex=ax)
ax2.plot( cis_coverage/ tot_coverage)
ax2.set_xlim([0, len(clr.bins()[:])])
ax2.set_ylabel('coverage ratio')
[13]:
Text(0, 0.5, 'coverage ratio')
Smoothing & Interpolation
When working with C data at high resolution, it is often useful to smooth matrices. cooltools provides a method, adaptive_coarsegrain, which adaptively smoothing corrected matrices based on the number of counts in raw matrices. For visualization it is also often useful to interpolate over filtered out bins.
[14]:
from cooltools.lib.numutils import adaptive_coarsegrain, interp_nan
clr_10kb = cooler.Cooler(f'{data_dir}/test.mcool::resolutions/10000')
start = 30_000_000
end = 35_000_000
region = ('chr17', start, end)
extents = (start, end, end, start)
cg = adaptive_coarsegrain(clr_10kb.matrix(balance=True).fetch(region),
clr_10kb.matrix(balance=False).fetch(region),
cutoff=3, max_levels=8)
cgi = interp_nan(cg)
f, axs = plt.subplots(
figsize=(18,5),
nrows=1,
ncols=3,
sharex=True, sharey=True)
ax = axs[0]
im = ax.matshow(clr_10kb.matrix(balance=True).fetch(region), cmap='fall', norm=norm, extent=extents)
ax.set_title('corrected')
ax = axs[1]
im2 = ax.matshow(cg, cmap='fall', norm=norm, extent=extents)
ax.set_title(f'adaptively coarsegrained')
ax = axs[2]
im3 = ax.matshow(cgi, cmap='fall', norm=norm, extent=extents)
ax.set_title(f'interpolated')
for ax in axs:
format_ticks(ax, rotate=False)
plt.colorbar(im3, ax=axs, fraction=0.046, label='corrected frequencies')
/home1/rahmanin/.conda/envs/open2c/lib/python3.9/site-packages/cooltools/lib/numutils.py:1376: RuntimeWarning: invalid value encountered in divide
val_cur = ar_cur / armask_cur
[14]:
<matplotlib.colorbar.Colorbar at 0x7f24dcaca730>
[15]:
### future:
# - yeast maps
# - translocations
# - higlass
This page was generated with nbsphinx from /home/docs/checkouts/readthedocs.org/user_builds/cooltools/checkouts/stable/docs/notebooks/viz.ipynb
Contacts vs distance
Welcome to the cooltools expected & contacts-vs-distance notebook!
In Hi-C maps, contact frequency decreases very strongly with genomic separation (also referred to as genomic distance). In the Hi-C field, this decay is often interchangeably referred to as the:
expected because one “expects” a certain average contact frequency at a given genomic separation
scaling which is borrowed from the polymer physics literature
P(s) curve contact probability, P, as a function of genomic separation, s.
The rate of decay of contacts with genomic separation reflects the polymeric nature of chromosomes and can tell us about the global folding patterns of the genome.
This decay has been observed to vary through the cell cycle, across cell types, and after degredation of structural maintenance of chromosomes complexes (SMCs) in both interphase and mitosis.
The goals of this notebook are to:
calculate the P(s) of a given cooler
plot the P(s) curve
smooth the P(s) curve with logarithmic binning
plot the derivative of P(s)
plot the P(s) between two different genomic regions
plot the matrix of average contact frequencies between different chromosomes
[1]:
%load_ext autoreload
%autoreload 2
[2]:
# import core packages
import warnings
warnings.filterwarnings("ignore")
from itertools import combinations
import os
# import semi-core packages
import matplotlib.pyplot as plt
from matplotlib import colors
%matplotlib inline
plt.style.use('seaborn-v0_8-poster')
import numpy as np
import pandas as pd
from multiprocessing import Pool
# import open2c libraries
import bioframe
import cooler
import cooltools
from packaging import version
if version.parse(cooltools.__version__) < version.parse('0.5.2'):
raise AssertionError("tutorial relies on cooltools version 0.5.2 or higher,"+
"please check your cooltools version and update to the latest")
# count cpus
num_cpus = os.getenv('SLURM_CPUS_PER_TASK')
if not num_cpus:
num_cpus = os.cpu_count()
num_cpus = int(num_cpus)
[3]:
# download test data
# this file is 145 Mb, and may take a few seconds to download
cool_file = cooltools.download_data("HFF_MicroC", cache=True, data_dir='./data/')
print(cool_file)
./data/test.mcool
[4]:
# Load a Hi-C map at a 1kb resolution from a cooler file.
resolution = 1000 # note this might be slightly slow on a laptop
# and could be lowered to 10kb for increased speed
clr = cooler.Cooler('data/test.mcool::/resolutions/'+str(resolution))
In addition to data stored in a cooler, the analyses below make use of where chromosomal arms start and stop to calculate contact frequency versus distance curves within arms. For commonly-used genomes, bioframe can be used to fetch these annotations directly from UCSC. For less commonly-used genomes, a table of arms, or chromosomes can be loaded in directly with pandas, e.g.
chromsizes = pd.read_csv('chrom.sizes', sep='\t')
Regions for calculating expected should be provided as a viewFrame, i.e. a dataframe with four columns, chrom, start, stop, name, where entries in the name column are unique and the intervals are non-overlapping. If the chromsizes table does not have a name column, it can be created with bioframe.core.construction.add_ucsc_name_column(bioframe.make_viewframe(chromsizes)).
[5]:
# Use bioframe to fetch the genomic features from the UCSC.
hg38_chromsizes = bioframe.fetch_chromsizes('hg38')
hg38_cens = bioframe.fetch_centromeres('hg38')
# create a view with chromosome arms using chromosome sizes and definition of centromeres
hg38_arms = bioframe.make_chromarms(hg38_chromsizes, hg38_cens)
# select only those chromosomes available in cooler
hg38_arms = hg38_arms[hg38_arms.chrom.isin(clr.chromnames)].reset_index(drop=True)
hg38_arms
[5]:
| chrom | start | end | name | |
|---|---|---|---|---|
| 0 | chr2 | 0 | 93900000 | chr2_p |
| 1 | chr2 | 93900000 | 242193529 | chr2_q |
| 2 | chr17 | 0 | 25100000 | chr17_p |
| 3 | chr17 | 25100000 | 83257441 | chr17_q |
Calculate the P(s) curve
To calculate the average contact frequency as a function of genomic separation, we use the fact that each diagonal of a Hi-C map records contacts between loci separated by the same genomic distance. For example, the 3rd diagonal of our matrix contains contacts between loci separated by 3-4kb (note that diagonals are 0-indexed). Thus, we calculate the average contact frequency, P(s), at a given genomic distance, s, as the average value of all pixels of the corresponding diagonal. This
operation is performed by cooltools.expected_cis.
Note that we calculate the P(s) separately for each chromosomal arm, by providing hg38_arms as a view_df. This way we will ignore contacts accross the centromere, which is generally a good idea, since such contacts have a slightly different decay versus genomic separation.
[6]:
# cvd == contacts-vs-distance
cvd = cooltools.expected_cis(
clr=clr,
view_df=hg38_arms,
smooth=False,
aggregate_smoothed=False,
nproc=num_cpus #if you do not have multiple cores available, set to 1
)
INFO:root:creating a Pool of 10 workers
This function calculates average contact frequency for raw and normalized interactions ( count.avg and balanced.avg) for each diagonal and each regions in the hg38_arms of a Hi-C map. It aslo keeps the sum of raw and normalized interaction counts (count.sum and balanced.sum) as well as the number of valid (i.e. non-masked) pixels at each diagonal, n_valid.
[7]:
display(cvd.head(4))
display(cvd.tail(4))
| region1 | region2 | dist | dist_bp | contact_frequency | n_total | n_valid | count.sum | balanced.sum | count.avg | balanced.avg | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr2_p | chr2_p | 0 | 0 | NaN | 93900 | 86055 | NaN | NaN | NaN | NaN |
| 1 | chr2_p | chr2_p | 1 | 1000 | NaN | 93899 | 85282 | NaN | NaN | NaN | NaN |
| 2 | chr2_p | chr2_p | 2 | 2000 | 0.098270 | 93898 | 84918 | 10842540.0 | 8344.916674 | 115.471469 | 0.098270 |
| 3 | chr2_p | chr2_p | 3 | 3000 | 0.042805 | 93897 | 84649 | 4733321.0 | 3623.417357 | 50.409715 | 0.042805 |
| region1 | region2 | dist | dist_bp | contact_frequency | n_total | n_valid | count.sum | balanced.sum | count.avg | balanced.avg | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 325448 | chr17_q | chr17_q | 58154 | 58154000 | NaN | 4 | 0 | 0.0 | 0.0 | 0.0 | NaN |
| 325449 | chr17_q | chr17_q | 58155 | 58155000 | NaN | 3 | 0 | 0.0 | 0.0 | 0.0 | NaN |
| 325450 | chr17_q | chr17_q | 58156 | 58156000 | NaN | 2 | 0 | 0.0 | 0.0 | 0.0 | NaN |
| 325451 | chr17_q | chr17_q | 58157 | 58157000 | NaN | 1 | 0 | 0.0 | 0.0 | 0.0 | NaN |
Note that the data from the first couple of diagonals are masked. This is done intentionally, since interactions at these diagonals (very short-ranged) are contaminated by non-informative Hi-C byproducts - dangling ends and self-circles.
Plot the P(s) curve
Time to plot P(s) !
The first challenge is that Hi-C has a very wide dynamic range. Hi-C probes genomic separations ranging from 100s to 100,000,000s of basepairs and contact frequencies also tend to span many orders of magnitude.
Plotting such data in the linear scale would reveal only a part of the whole picture. Instead, we typically switch to double logarithmic (aka log-log) plots, where the x and y coordinates vary by orders of magnitude.
With the flags used above, expected_cis() does not smooth or aggregate across regions. This can lead to noisy P(s) curves for each region:
[8]:
f, ax = plt.subplots(1,1)
for region in hg38_arms['name']:
ax.loglog(
cvd['dist_bp'].loc[cvd['region1']==region],
cvd['contact_frequency'].loc[cvd['region1']==region],
)
ax.set(
xlabel='separation, bp',
ylabel='IC contact frequency')
ax.set_aspect(1.0)
ax.grid(lw=0.5)
The non-smoothed curves plotted above form characteristic “fans” at longer separations. This happens for two reasons: (a) we plot values of each diagonal separately and thus each decade of s contains 10x more points, and (b) due to the polymer nature of chromosomes, contact frequency at large genomic separations are lower and thus more affected by sequencing depth.
This issue is more that just cosmetic, as this noise would prevent us from doing finer analyses of P(s) and propagate into data derived from P(s). However, there is a simple solution: we can smooth P(s) over multiple diagonals. This works because P(s) changes very gradually with s, so that consecutive diagonals have similar values. Furthermore, we can make each subsequent smoothing window wider than the previous one, so that each order of magnitude of genomic separation contains the
same number of windows. Such aggregation is a little tricky to perform, so cooltools.expected implements this operation.
Smoothing & aggregating P(s) curves
Instead of the flags above, we can pass flags to expected_cis() that return smoothed and aggregated columns for futher analysis (which are on by default).
Note that the plots below use smooth_sigma=0.1, which is relatively conservative, and this parameter can be lowered (with discretion) for sufficiently high-resolution datasets.
[9]:
cvd_smooth_agg = cooltools.expected_cis(
clr=clr,
view_df=hg38_arms,
smooth=True,
aggregate_smoothed=True,
smooth_sigma=0.1,
nproc=num_cpus
)
INFO:root:creating a Pool of 10 workers
[10]:
display(cvd_smooth_agg.head(4))
| region1 | region2 | dist | dist_bp | contact_frequency | n_total | n_valid | count.sum | balanced.sum | count.avg | balanced.avg | balanced.avg.smoothed | balanced.avg.smoothed.agg | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr2_p | chr2_p | 0 | 0 | NaN | 93900 | 86055 | NaN | NaN | NaN | NaN | NaN | NaN |
| 1 | chr2_p | chr2_p | 1 | 1000 | 0.001060 | 93899 | 85282 | NaN | NaN | NaN | NaN | 0.001043 | 0.001060 |
| 2 | chr2_p | chr2_p | 2 | 2000 | 0.088615 | 93898 | 84918 | 10842540.0 | 8344.916674 | 115.471469 | 0.098270 | 0.087228 | 0.088615 |
| 3 | chr2_p | chr2_p | 3 | 3000 | 0.043947 | 93897 | 84649 | 4733321.0 | 3623.417357 | 50.409715 | 0.042805 | 0.043116 | 0.043947 |
[11]:
cvd_smooth_agg['balanced.avg.smoothed'].loc[cvd_smooth_agg['dist'] < 2] = np.nan
f, ax = plt.subplots(1,1)
for region in hg38_arms['name']:
ax.loglog(
cvd_smooth_agg['dist_bp'].loc[cvd_smooth_agg['region1']==region],
cvd_smooth_agg['balanced.avg.smoothed'].loc[cvd_smooth_agg['region1']==region],
)
ax.set(
xlabel='separation, bp',
ylabel='IC contact frequency')
ax.set_aspect(1.0)
ax.grid(lw=0.5)
The balanced.avg.smoothed.agg is averaged across regions, and shows the same exact curve for each.
[12]:
cvd_smooth_agg['balanced.avg.smoothed.agg'].loc[cvd_smooth_agg['dist'] < 2] = np.nan
f, ax = plt.subplots(1,1)
for region in hg38_arms['name']:
ax.loglog(
cvd_smooth_agg['dist_bp'].loc[cvd_smooth_agg['region1']==region],
cvd_smooth_agg['balanced.avg.smoothed.agg'].loc[cvd_smooth_agg['region1']==region],
)
ax.set(
xlabel='separation, bp',
ylabel='IC contact frequency')
ax.set_aspect(1.0)
ax.grid(lw=0.5)
Plot the smoothed P(s) curve and its derivative
Logbin-smoothing of P(s) reduces the “fanning” at longer s and enables us to plot the derivative of the P(s) curve in the log-log space. This derivative is extremely informative, as it can be compared to predictions from various polymer models.
[13]:
# Just take a single value for each genomic separation
cvd_merged = cvd_smooth_agg.drop_duplicates(subset=['dist'])[['dist_bp', 'balanced.avg.smoothed.agg']]
[14]:
# Calculate derivative in log-log space
der = np.gradient(np.log(cvd_merged['balanced.avg.smoothed.agg']),
np.log(cvd_merged['dist_bp']))
[15]:
f, axs = plt.subplots(
figsize=(6.5,13),
nrows=2,
gridspec_kw={'height_ratios':[6,2]},
sharex=True)
ax = axs[0]
ax.loglog(
cvd_merged['dist_bp'],
cvd_merged['balanced.avg.smoothed.agg'],
'-'
)
ax.set(
ylabel='IC contact frequency',
xlim=(1e3,1e8)
)
ax.set_aspect(1.0)
ax.grid(lw=0.5)
ax = axs[1]
ax.semilogx(
cvd_merged['dist_bp'],
der,
alpha=0.5
)
ax.set(
xlabel='separation, bp',
ylabel='slope')
ax.grid(lw=0.5)
Plot the P(s) curve for interactions between different regions.
Finally, we can plot P(s) curves for contacts between loci that belong to different regions.
A commonly considered situation is for trans-arm interactions, i.e. contacts between loci on the opposite side of a centromere. Such P(s) can be calculated via cooltools.expected_cis by passing intra_only=False.
[16]:
# cvd_inter == contacts-vs-distance between chromosomal arms
cvd_inter = cooltools.expected_cis(
clr=clr,
view_df=hg38_arms,
intra_only=False,
nproc=num_cpus
)
# select only inter-arm interactions:
cvd_inter = cvd_inter[ cvd_inter["region1"] != cvd_inter["region2"] ].reset_index(drop=True)
INFO:root:creating a Pool of 10 workers
[17]:
cvd_inter['balanced.avg.smoothed.agg'].loc[cvd_inter['dist'] < 2] = np.nan
f, ax = plt.subplots(1,1,
figsize=(5,5),)
ax.loglog(
cvd_inter['dist_bp'],
cvd_inter['balanced.avg.smoothed.agg'],
)
ax.set(
xlabel='separation, bp',
ylabel='IC contact frequency',
title="average interactions between chromosomal arms")
ax.grid(lw=0.5)
ax.set_aspect(1.0)
Averaging interaction frequencies in blocks
For trans (i.e. inter-chromosomal) interactions, the notion of “genomic separation” becomes irrelevant, as loci on different chromosomes are not connected by any polymer chain. Thus, the “expected” level of trans interactions is a scalar, the average interaction frequency for a given pair of chromosomes.
Note that this sample dataset only includes two chromosomes– the heatmap of pairwise average contact frequencies can appear much more interesting for a greater number of chromosomes.
[18]:
# average contacts, in this case between pairs of chromosomal arms:
ac = cooltools.expected_trans(
clr,
view_df = None, # full chromosomes as the view
nproc=num_cpus
)
# average raw interaction counts and normalized contact frequencies are already in the result
ac
INFO:root:creating a Pool of 10 workers
[18]:
| region1 | region2 | n_valid | count.sum | balanced.sum | count.avg | balanced.avg | |
|---|---|---|---|---|---|---|---|
| 0 | chr2 | chr17 | 16604223614 | 1307071.0 | 1021.728671 | 0.000079 | 6.153426e-08 |
[19]:
# pivot a table to generate a pair-wise average interaction heatmap:
acp = (ac
.pivot_table(values="balanced.avg",
index="region1",
columns="region2",
observed=True)
.reindex(index=clr.chromnames,
columns=clr.chromnames)
)
[20]:
fs = 14
f, axs = plt.subplots(
figsize=(6.0,5.5),
ncols=2,
gridspec_kw={'width_ratios':[20,1],"wspace":0.1},
)
# assign heatmap and colobar axis:
ax, cax = axs
# draw a heatmap, using log-scale for interaction freq-s:
acpm = ax.imshow(
acp,
cmap="YlOrRd",
norm=colors.LogNorm(),
aspect=1.0
)
# assign ticks and labels (ordered names of chromosome arms):
ax.set(
xticks=range(len(clr.chromnames)),
yticks=range(len(clr.chromnames)),
title="average interactions\nbetween chromosomes",
)
ax.set_xticklabels(
clr.chromnames,
rotation=30,
horizontalalignment='right',
fontsize=fs
)
ax.set_yticklabels(
clr.chromnames,
fontsize=fs
)
# draw a colorbar of interaction frequencies for the heatmap:
f.colorbar(
acpm,
cax=cax,
label='IC contact frequency'
)
# draw a grid around values:
ax.set_xticks(
[x-0.5 for x in range(1,len(clr.chromnames))],
minor=True
)
ax.set_yticks(
[y-0.5 for y in range(1,len(clr.chromnames))],
minor=True
)
ax.grid(which="minor")
Impact of sequencing depth on computed P(s)
We explore the influence of sequencing coverage on calculating P(s) curves using cooltools.sample() to generate downsampled coolers from the Kreitenstein microC test dataset. We then compute raw P(s) and smoothed P(s) at various levels of downsampling, for the q arm of chr2.
Raw P(s) appear very noisy even with 0.1% downsampling. Smoothed P(s) are fairly consistent down to 0.01% downsampling. Derivatives, however, are less reliable at 0.01% downsampling.
[31]:
# create downsampled test data
downsampling_fracs = [0.0001, 0.001]
num_reads = {}
cvds = {}
cvds_smoothed = {}
derivs_smoothed = {}
p = Pool(num_cpus)
for frac in downsampling_fracs:
cooltools.sample(clr, out_clr_path=f'./data/test_sampled_{frac}_.cool', frac=frac, nproc=num_cpus)
clr_downsampled = cooler.Cooler(f'./data/test_sampled_{frac}_.cool')
result = cooler.balance_cooler(clr_downsampled, map=p.map, store=True, min_nnz=0)
p.close()
p.terminate()
INFO:root:creating a Pool of 10 workers
INFO:root:creating a Pool of 10 workers
[32]:
# expected & derivative calculation for raw data, using only the second arm of chr2
cvd_smooth_agg_raw = cooltools.expected_cis(
clr=clr,
view_df=hg38_arms[1:2],
clr_weight_name=None,
smooth=True,
aggregate_smoothed=True,
nproc=num_cpus
)
cvd_smooth_agg_raw['count.avg.smoothed'].loc[cvd_smooth_agg_raw['dist'] < 2] = np.nan
cvd_merged = cvd_smooth_agg_raw.drop_duplicates(subset=['dist'])[['dist_bp', 'count.avg.smoothed.agg']]
der = np.gradient(np.log(cvd_merged['count.avg.smoothed.agg']),
np.log(cvd_merged['dist_bp']))
deriv_smoothed_raw = der
cvds[1.0] = cvd_smooth_agg_raw.copy()
cvds_smoothed[1.0]= cvd_smooth_agg_raw.copy()
num_reads[1.0] = cvd_smooth_agg_raw['count.sum'].sum().astype(int)
derivs_smoothed[1.0] = deriv_smoothed_raw
INFO:root:creating a Pool of 10 workers
[39]:
# expected calculation for the downsampled data
for frac in downsampling_fracs:
clr_downsampled = cooler.Cooler(f'./data/test_sampled_{frac}_.cool')
cvd_downsampled = cooltools.expected_cis(
clr=clr_downsampled,
view_df=hg38_arms[1:2],
clr_weight_name=None,
smooth=False,
aggregate_smoothed=False,
nproc=num_cpus #if you do not have multiple cores available, set to 1
)
cvds[frac] = cvd_downsampled
num_reads[frac] = cvd_downsampled['count.sum'].sum().astype(int)
INFO:root:creating a Pool of 10 workers
INFO:root:creating a Pool of 10 workers
[42]:
f, ax = plt.subplots(1,1, figsize=(8, 8))
region = hg38_arms['name'][0]
for frac in [1]+downsampling_fracs:
cvd_downsampled = cvds[frac]
ax.loglog(
cvd_downsampled['dist_bp'],
cvd_downsampled['count.avg'],
label=f'{frac*100}%, {num_reads[frac]} reads',
)
ax.set(
xlabel='separation, bp',
ylabel='contact frequency')
ax.grid(lw=0.5)
ax.legend()
ax.title.set_text(region)
ax.set_ylim(ymin=10**(-8))
f.show()
[43]:
# expected calculation for the smoothed data
for frac in downsampling_fracs:
clr_downsampled = cooler.Cooler(f'./data/test_sampled_{frac}_.cool')
cvd_smooth_agg_downsampled = cooltools.expected_cis(
clr=clr_downsampled,
view_df=hg38_arms[1:2],
clr_weight_name=None,
smooth=True,
aggregate_smoothed=True,
nproc=num_cpus
)
cvd_smooth_agg_downsampled['count.avg.smoothed'].loc[cvd_smooth_agg_downsampled['dist'] < 2] = np.nan
cvds_smoothed[frac] = cvd_smooth_agg_downsampled
cvd_merged = cvd_smooth_agg_downsampled.drop_duplicates(subset=['dist'])[['dist_bp', 'count.avg.smoothed.agg']]
der = np.gradient(np.log(cvd_merged['count.avg.smoothed.agg']),
np.log(cvd_merged['dist_bp']))
derivs_smoothed[frac] = der
INFO:root:creating a Pool of 10 workers
INFO:root:creating a Pool of 10 workers
[47]:
f, ax = plt.subplots(1,1,figsize=(8, 8))
for frac in [1]+downsampling_fracs:
cvd_smooth_agg_downsampled = cvds_smoothed[frac]
cvd_smooth_agg_downsampled['count.avg.smoothed'].loc[cvd_smooth_agg_downsampled['dist'] < 2] = np.nan
ax.loglog(
cvd_smooth_agg_downsampled['dist_bp'],
cvd_smooth_agg_downsampled['count.avg.smoothed'],
label=f'{frac*100}%, {num_reads[frac]} reads')
ax.set(
xlabel='separation, bp',
ylabel='contact frequency')
ax.grid(lw=0.5)
ax.title.set_text(region)
ax.legend()
ax.set_ylim(ymin=10**(-8))
f.show()
[56]:
f, ax = plt.subplots(1,1,figsize=(8,3))
for frac in [1]+downsampling_fracs:
der = derivs_smoothed[frac]
der[3] = np.nan
ax.semilogx(
cvd_smooth_agg_downsampled['dist_bp'],
der,
label=f'{frac*100}%, {num_reads[frac]} reads'
)
ax.set(
xlabel='separation, bp',
ylabel='slope')
ax.grid(lw=0.5)
ax.title.set_text(region)
ax.legend(loc='center left', bbox_to_anchor=(1, 0.5))
plt.ylim(-2.25,.25)
f.show()
This page was generated with nbsphinx from /home/docs/checkouts/readthedocs.org/user_builds/cooltools/checkouts/stable/docs/notebooks/contacts_vs_distance.ipynb
Compartments & Saddleplots
Welcome to the compartments and saddleplot notebook!
This notebook illustrates cooltools functions used for investigating chromosomal compartments, visible as plaid patterns in mammalian interphase contact frequency maps.
These plaid patterns reflect tendencies of chromosome regions to make more frequent contacts with regions of the same type: active regions have increased contact frequency with other active regions, and intactive regions tend to contact other inactive regions more frequently. The strength of compartmentalization has been show to vary through the cell cycle, across cell types, and after degredation of components of the cohesin complex.
In this notebook we:
obtain compartment profiles using eigendecomposition
calculate and visualize strength of compartmentalization using saddleplots
[1]:
# import standard python libraries
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
import pandas as pd
import os, subprocess
[2]:
# Import python package for working with cooler files and tools for analysis
import cooler
import cooltools.lib.plotting
[3]:
from packaging import version
if version.parse(cooltools.__version__) < version.parse('0.5.4'):
raise AssertionError("tutorials rely on cooltools version 0.5.4 or higher,"+
"please check your cooltools version and update to the latest")
[4]:
# download test data
# this file is 145 Mb, and may take a few seconds to download
import cooltools
cool_file = cooltools.download_data("HFF_MicroC", cache=True, data_dir='./data/')
print(cool_file)
./data/test.mcool
Calculating per-chromosome compartmentalization
We first load the Hi-C data at 100 kbp resolution.
Note that the current implementation of eigendecomposition in cooltools assumes that individual regions can be held in memory– for hg38 at 100kb this is either a 2422x2422 matrix for chr2, or a 3255x3255 matrix for the full cooler here.
[5]:
clr = cooler.Cooler('./data/test.mcool::resolutions/100000')
Since the orientation of eigenvectors is determined up to a sign, the convention for Hi-C data anaylsis is to orient eigenvectors to be positively correlated with a binned profile of GC content as a ‘phasing track’.
In humans and mice, GC content is useful for phasing because it typically has a strong correlation at the 100kb-1Mb bin level with the eigenvector. In other organisms, other phasing tracks have been used to orient eigenvectors from Hi-C data.
For other data analyses, different conventions are used to consistently orient eigenvectors. For example, spectral clustering as implemented in scikit-learn orients vectors such that the absolute maximum element of each vector is positive.
[ ]:
## fasta sequence is required for calculating binned profile of GC conent
if not os.path.isfile('./hg38.fa'):
## note downloading a ~1Gb file can take a minute
subprocess.call('wget --progress=bar:force:noscroll https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.fa.gz', shell=True)
subprocess.call('gunzip hg38.fa.gz', shell=True)
[7]:
import bioframe
bins = clr.bins()[:]
hg38_genome = bioframe.load_fasta('./hg38.fa');
## note the next command may require installing pysam
gc_cov = bioframe.frac_gc(bins[['chrom', 'start', 'end']], hg38_genome)
gc_cov.to_csv('hg38_gc_cov_100kb.tsv',index=False,sep='\t')
display(gc_cov)
| chrom | start | end | GC | |
|---|---|---|---|---|
| 0 | chr2 | 0 | 100000 | 0.435867 |
| 1 | chr2 | 100000 | 200000 | 0.409530 |
| 2 | chr2 | 200000 | 300000 | 0.421890 |
| 3 | chr2 | 300000 | 400000 | 0.431870 |
| 4 | chr2 | 400000 | 500000 | 0.458610 |
| ... | ... | ... | ... | ... |
| 3250 | chr17 | 82800000 | 82900000 | 0.528210 |
| 3251 | chr17 | 82900000 | 83000000 | 0.518530 |
| 3252 | chr17 | 83000000 | 83100000 | 0.561450 |
| 3253 | chr17 | 83100000 | 83200000 | 0.535119 |
| 3254 | chr17 | 83200000 | 83257441 | 0.473451 |
3255 rows × 4 columns
Cooltools also allows a view to be passed for eigendecomposition to limit to a certain set of regions. The following code creates the simplest view, of the two chromosomes in this cooler.
[8]:
view_df = pd.DataFrame({'chrom': clr.chromnames,
'start': 0,
'end': clr.chromsizes.values,
'name': clr.chromnames}
)
display(view_df)
| chrom | start | end | name | |
|---|---|---|---|---|
| 0 | chr2 | 0 | 242193529 | chr2 |
| 1 | chr17 | 0 | 83257441 | chr17 |
To capture the pattern of compartmentalization within-chromosomes, in cis, cooltools eigs_cis first removes the dependence of contact frequency by distance, and then performs eigenedecompostion.
[9]:
# obtain first 3 eigenvectors
cis_eigs = cooltools.eigs_cis(
clr,
gc_cov,
view_df=view_df,
n_eigs=3,
)
# cis_eigs[0] returns eigenvalues, here we focus on eigenvectors
eigenvector_track = cis_eigs[1][['chrom','start','end','E1']]
Plotting the first eigenvector next to the Hi-C map allows us to see how this captures the plaid pattern.
To better visualize this relationship, we overlay the map with a binary segmentation of the eigenvector. Eigenvectors can be segmented by a variety of methods. The simplest segmentation, shown here, is to simply binarize eigenvectors, and term everything above zero the “A-compartment” and everything below 0 the “B-compartment”.
[10]:
from matplotlib.colors import LogNorm
from mpl_toolkits.axes_grid1 import make_axes_locatable
f, ax = plt.subplots(
figsize=(15, 10),
)
norm = LogNorm(vmax=0.1)
im = ax.matshow(
clr.matrix()[:],
norm=norm,
cmap='fall'
);
plt.axis([0,500,500,0])
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.1)
plt.colorbar(im, cax=cax, label='corrected frequencies');
ax.set_ylabel('chr2:0-50Mb')
ax.xaxis.set_visible(False)
ax1 = divider.append_axes("top", size="20%", pad=0.25, sharex=ax)
weights = clr.bins()[:]['weight'].values
ax1.plot([0,500],[0,0],'k',lw=0.25)
ax1.plot( eigenvector_track['E1'].values, label='E1')
ax1.set_ylabel('E1')
ax1.set_xticks([]);
for i in np.where(np.diff( (cis_eigs[1]['E1']>0).astype(int)))[0]:
ax.plot([0, 500],[i,i],'k',lw=0.5)
ax.plot([i,i],[0, 500],'k',lw=0.5)
Saddleplots
A common way to visualize preferences captured by the eigenvector is by using saddleplots.
To generate a saddleplot, we first use the eigenvector to stratify genomic regions into groups with similar values of the eigenvector. These groups are then averaged over to create the saddleplot. This process is called “digitizing”.
Cooltools will operate with digitized bedgraph-like track with four columns. The fourth, or value, column is a categorical, as shown above for the first three bins. Categories have the following encoding:
- `1..n` <-> values assigned to bins defined by vrange or qrange
- `0` <-> left outlier values
- `n+1` <-> right outlier values
- `-1` <-> missing data (NaNs)
Track values can either be digitized by numeric values, by passing vrange, or by quantiles, by passing qrange, as above.
To create saddles in cis with saddle, cooltools requires: a cooler, a table with expected as function of distance, and parameters for digitizing:
[11]:
cvd = cooltools.expected_cis(
clr=clr,
view_df=view_df,
)
[12]:
Q_LO = 0.025 # ignore 2.5% of genomic bins with the lowest E1 values
Q_HI = 0.975 # ignore 2.5% of genomic bins with the highest E1 values
N_GROUPS = 38 # divide remaining 95% of the genome into 38 equisized groups, 2.5% each
saddle then returns two matrices: one with the sum for each pair of categories, interaction_sum, and the other with the number of bins for each pair of categories, interaction_count. Typically, interaction_sum/interaction_count is visualized.
[13]:
interaction_sum, interaction_count = cooltools.saddle(
clr,
cvd,
eigenvector_track,
'cis',
n_bins=N_GROUPS,
qrange=(Q_LO,Q_HI),
view_df=view_df
)
There are multiple ways to plot saddle data, one useful way is shown below.
This visualization includes histograms of the number of bins contributing to each row/column of the saddleplot.
[14]:
import warnings
from cytoolz import merge
def saddleplot(
track,
saddledata,
n_bins,
vrange=None,
qrange=(0.0, 1.0),
cmap="coolwarm",
scale="log",
vmin=0.5,
vmax=2,
color=None,
title=None,
xlabel=None,
ylabel=None,
clabel=None,
fig=None,
fig_kws=None,
heatmap_kws=None,
margin_kws=None,
cbar_kws=None,
subplot_spec=None,
):
"""
Generate a saddle plot.
Parameters
----------
track : pd.DataFrame
See cooltools.digitize() for details.
saddledata : 2D array-like
Saddle matrix produced by `make_saddle`. It will include 2 flanking
rows/columns for outlier signal values, thus the shape should be
`(n+2, n+2)`.
cmap : str or matplotlib colormap
Colormap to use for plotting the saddle heatmap
scale : str
Color scaling to use for plotting the saddle heatmap: log or linear
vmin, vmax : float
Value limits for coloring the saddle heatmap
color : matplotlib color value
Face color for margin bar plots
fig : matplotlib Figure, optional
Specified figure to plot on. A new figure is created if none is
provided.
fig_kws : dict, optional
Passed on to `plt.Figure()`
heatmap_kws : dict, optional
Passed on to `ax.imshow()`
margin_kws : dict, optional
Passed on to `ax.bar()` and `ax.barh()`
cbar_kws : dict, optional
Passed on to `plt.colorbar()`
subplot_spec : GridSpec object
Specify a subregion of a figure to using a GridSpec.
Returns
-------
Dictionary of axes objects.
"""
# warnings.warn(
# "Generating a saddleplot will be deprecated in future versions, "
# + "please see https://github.com/open2c_examples for examples on how to plot saddles.",
# DeprecationWarning,
# )
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
from matplotlib.colors import Normalize, LogNorm
from matplotlib import ticker
import matplotlib.pyplot as plt
class MinOneMaxFormatter(ticker.LogFormatter):
def set_locs(self, locs=None):
self._sublabels = set([vmin % 10 * 10, vmax % 10, 1])
def __call__(self, x, pos=None):
if x not in [vmin, 1, vmax]:
return ""
else:
return "{x:g}".format(x=x)
track_value_col = track.columns[3]
track_values = track[track_value_col].values
digitized_track, binedges = cooltools.digitize(
track, n_bins, vrange=vrange, qrange=qrange
)
x = digitized_track[digitized_track.columns[3]].values.astype(int).copy()
x = x[(x > -1) & (x < len(binedges) + 1)]
# Old version
# hist = np.bincount(x, minlength=len(binedges) + 1)
groupmean = track[track.columns[3]].groupby(digitized_track[digitized_track.columns[3]]).mean()
if qrange is not None:
lo, hi = qrange
binedges = np.linspace(lo, hi, n_bins + 1)
# Barplot of mean values and saddledata are flanked by outlier bins
n = saddledata.shape[0]
X, Y = np.meshgrid(binedges, binedges)
C = saddledata
if (n - n_bins) == 2:
C = C[1:-1, 1:-1]
groupmean = groupmean[1:-1]
# Layout
if subplot_spec is not None:
GridSpec = partial(GridSpecFromSubplotSpec, subplot_spec=subplot_spec)
grid = {}
gs = GridSpec(
nrows=3,
ncols=3,
width_ratios=[0.2, 1, 0.1],
height_ratios=[0.2, 1, 0.1],
wspace=0.05,
hspace=0.05,
)
# Figure
if fig is None:
fig_kws_default = dict(figsize=(5, 5))
fig_kws = merge(fig_kws_default, fig_kws if fig_kws is not None else {})
fig = plt.figure(**fig_kws)
# Heatmap
if scale == "log":
norm = LogNorm(vmin=vmin, vmax=vmax)
elif scale == "linear":
norm = Normalize(vmin=vmin, vmax=vmax)
else:
raise ValueError("Only linear and log color scaling is supported")
grid["ax_heatmap"] = ax = plt.subplot(gs[4])
heatmap_kws_default = dict(cmap="coolwarm", rasterized=True)
heatmap_kws = merge(
heatmap_kws_default, heatmap_kws if heatmap_kws is not None else {}
)
img = ax.pcolormesh(X, Y, C, norm=norm, **heatmap_kws)
plt.gca().yaxis.set_visible(False)
# Margins
margin_kws_default = dict(edgecolor="k", facecolor=color, linewidth=1)
margin_kws = merge(margin_kws_default, margin_kws if margin_kws is not None else {})
# left margin hist
grid["ax_margin_y"] = plt.subplot(gs[3], sharey=grid["ax_heatmap"])
plt.barh(
binedges, height=1/len(binedges), width=groupmean, align="edge", **margin_kws
)
plt.xlim(plt.xlim()[1], plt.xlim()[0]) # fliplr
plt.ylim(hi, lo)
plt.gca().spines["top"].set_visible(False)
plt.gca().spines["bottom"].set_visible(False)
plt.gca().spines["left"].set_visible(False)
plt.gca().xaxis.set_visible(False)
# top margin hist
grid["ax_margin_x"] = plt.subplot(gs[1], sharex=grid["ax_heatmap"])
plt.bar(
binedges, width=1/len(binedges), height=groupmean, align="edge", **margin_kws
)
plt.xlim(lo, hi)
# plt.ylim(plt.ylim()) # correct
plt.gca().spines["top"].set_visible(False)
plt.gca().spines["right"].set_visible(False)
plt.gca().spines["left"].set_visible(False)
plt.gca().xaxis.set_visible(False)
plt.gca().yaxis.set_visible(False)
# # Colorbar
grid["ax_cbar"] = plt.subplot(gs[5])
cbar_kws_default = dict(fraction=0.8, label=clabel or "")
cbar_kws = merge(cbar_kws_default, cbar_kws if cbar_kws is not None else {})
if scale == "linear" and vmin is not None and vmax is not None:
grid["ax_cbar"] = cb = plt.colorbar(img, **cbar_kws)
# cb.set_ticks(np.arange(vmin, vmax + 0.001, 0.5))
# # do linspace between vmin and vmax of 5 segments and trunc to 1 decimal:
decimal = 10
nsegments = 5
cd_ticks = np.trunc(np.linspace(vmin, vmax, nsegments) * decimal) / decimal
cb.set_ticks(cd_ticks)
else:
print('cbar')
cb = plt.colorbar(img, format=MinOneMaxFormatter(), cax=grid["ax_cbar"], **cbar_kws)
cb.ax.yaxis.set_minor_formatter(MinOneMaxFormatter())
# extra settings
grid["ax_heatmap"].set_xlim(lo, hi)
grid["ax_heatmap"].set_ylim(hi, lo)
grid['ax_heatmap'].grid(False)
if title is not None:
grid["ax_margin_x"].set_title(title)
if xlabel is not None:
grid["ax_heatmap"].set_xlabel(xlabel)
if ylabel is not None:
grid["ax_margin_y"].set_ylabel(ylabel)
return grid
The saddle below shows average observed/expected contact frequency between regions grouped according to their digitized eigenvector values with a blue-to-white-to-red colormap. Inactive regions (i.e. low digitized values) are on the top and left, and active regions (i.e. high digitized values) are on the bottom and right.
The saddleplot shows that inactive regions are enriched for contact frequency with other inactive regions (red area in the upper left), and active regions are enriched for contact frequency with other active regions (red area in the lower right). In contrast, active regions are depleted for contact frequency with inactive regions (blue area in top right and bottom left).
[15]:
saddleplot(eigenvector_track,
interaction_sum/interaction_count,
N_GROUPS,
qrange=(Q_LO,Q_HI),
cbar_kws={'label':'average observed/expected contact frequency'}
);
cbar
Saddle strength
Comparing the average obs/expected values between active and inactive chromatin, is one useful measure of the strength of compartmentalization. This can be measured with saddle_strength(), which can be thought of as taking the ratio between (AA+BB) / (AB+BA). This corresponds visually to the ratio between the upper left and lower right corners, versus the lower left and upper right corners in the plot above.
[16]:
from cooltools.api.saddle import saddle_strength
# at extent=0, this reduces to ((S/C)[0,0] + (S/C)[-1,-1]) / (2*(S/C)[-1,0])
x = np.arange(N_GROUPS + 2)
plt.step(x, saddle_strength(interaction_sum, interaction_count), where='pre')
plt.xlabel('extent')
plt.ylabel('(AA + BB) / (AB + BA)')
plt.title('saddle strength profile')
plt.axhline(0, c='grey', ls='--', lw=1) # Q: is there a reason this is 0 not 1?
plt.xlim(0, len(x)//2); # Q: is this less intuitive than showing for all x, as it converges to no difference (i.e. 1)?
This page was generated with nbsphinx from /home/docs/checkouts/readthedocs.org/user_builds/cooltools/checkouts/stable/docs/notebooks/compartments_and_saddles.ipynb
Insulation & boundaries
Welcome to the contact insulation notebook!
Insulation is a simple concept, yet a powerful way to look at C data. Insulation is one aspect of locus-specific contact frequency at small genomic distances, and reflects the segmentation of the genome into domains.
Insulation can be computed with multiple methods. One of the most common methods involves using a diamond-window score to generate an insulation profile. To compute this profile, slide a diamond-shaped window along the genome, with one of the corners on the main diagonal of the matrix, and sum up the contacts within the window for each position.
Insulation profiles reveal that certain locations have lower scores, reflecting lowered contact frequencies between upstream and downstream loci. These positions are often referred to as boundaries, and are also obtained with multiple methods. Here we illustrate one thresholding method for determining boundaries from an insulation profile.
In this notebook we:
Calculate the insulation score genome-wide and display it alongside an interaction matrix
Call insulating boundaries
Filter insulating boundaries based on their strength
Calculate enrichment of CTCF/genes at boundaries
Repeat boundary filtering based on enrichmnent of CTCF, a known insulator protein in mammalian genomes
[1]:
# import standard python libraries
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
[2]:
# Import python package for working with cooler files and tools for analysis
import cooler
import cooltools.lib.plotting
from cooltools import insulation
from packaging import version
if version.parse(cooltools.__version__) < version.parse('0.5.4'):
raise AssertionError("tutorials rely on cooltools version 0.5.4 or higher,"+
"please check your cooltools version and update to the latest")
[3]:
# download test data
# this file is 145 Mb, and may take a few seconds to download
import cooltools
data_dir = './data/'
cool_file = cooltools.download_data("HFF_MicroC", cache=True, data_dir=data_dir)
print(cool_file)
./data/test.mcool
Calculating genome-wide contact insulation
Here we load the Hi-C data at 10 kbp resolution and calculate insulation score with 4 different window sizes
[4]:
resolution = 10000
clr = cooler.Cooler(f'{data_dir}test.mcool::resolutions/{resolution}')
windows = [3*resolution, 5*resolution, 10*resolution, 25*resolution]
insulation_table = insulation(clr, windows, verbose=True)
INFO:root:fallback to serial implementation.
INFO:root:Processing region chr2
INFO:root:Processing region chr17
This function returns a dataframe where rows correspond to genomic bins of the cooler.
The columns of this insulation dataframe report the insulation score, the number of valid (non-nan) pixels, whether the given bin is valid, the boundary prominence (strength) and whether locus is called as a boundary after thresholding, for each of the window sizes provided to the function.
Below we print the information returned for any window size, as well as the specific information for the largest window used:
[5]:
first_window_summary =insulation_table.columns[[ str(windows[-1]) in i for i in insulation_table.columns]]
insulation_table[['chrom','start','end','region','is_bad_bin']+list(first_window_summary)].iloc[1000:1005]
[5]:
| chrom | start | end | region | is_bad_bin | log2_insulation_score_250000 | n_valid_pixels_250000 | boundary_strength_250000 | is_boundary_250000 | |
|---|---|---|---|---|---|---|---|---|---|
| 1000 | chr2 | 10000000 | 10010000 | chr2 | False | 0.309791 | 622.0 | NaN | False |
| 1001 | chr2 | 10010000 | 10020000 | chr2 | False | 0.226045 | 622.0 | NaN | False |
| 1002 | chr2 | 10020000 | 10030000 | chr2 | False | 0.090809 | 622.0 | NaN | False |
| 1003 | chr2 | 10030000 | 10040000 | chr2 | False | -0.101091 | 622.0 | NaN | False |
| 1004 | chr2 | 10040000 | 10050000 | chr2 | False | -0.342858 | 622.0 | NaN | False |
[6]:
# Functions to help with plotting
def pcolormesh_45deg(ax, matrix_c, start=0, resolution=1, *args, **kwargs):
start_pos_vector = [start+resolution*i for i in range(len(matrix_c)+1)]
import itertools
n = matrix_c.shape[0]
t = np.array([[1, 0.5], [-1, 0.5]])
matrix_a = np.dot(np.array([(i[1], i[0])
for i in itertools.product(start_pos_vector[::-1],
start_pos_vector)]), t)
x = matrix_a[:, 1].reshape(n + 1, n + 1)
y = matrix_a[:, 0].reshape(n + 1, n + 1)
im = ax.pcolormesh(x, y, np.flipud(matrix_c), *args, **kwargs)
im.set_rasterized(True)
return im
from matplotlib.ticker import EngFormatter
bp_formatter = EngFormatter('b')
def format_ticks(ax, x=True, y=True, rotate=True):
if y:
ax.yaxis.set_major_formatter(bp_formatter)
if x:
ax.xaxis.set_major_formatter(bp_formatter)
ax.xaxis.tick_bottom()
if rotate:
ax.tick_params(axis='x',rotation=45)
Let’s see what the insulation track at the highest resolution looks like, next to a rotated Hi-C matrix.
[7]:
from matplotlib.colors import LogNorm
from mpl_toolkits.axes_grid1 import make_axes_locatable
import bioframe
plt.rcParams['font.size'] = 12
start = 10_500_000
end = start+ 90*windows[0]
region = ('chr2', start, end)
norm = LogNorm(vmax=0.1, vmin=0.001)
data = clr.matrix(balance=True).fetch(region)
f, ax = plt.subplots(figsize=(18, 6))
im = pcolormesh_45deg(ax, data, start=region[1], resolution=resolution, norm=norm, cmap='fall')
ax.set_aspect(0.5)
ax.set_ylim(0, 10*windows[0])
format_ticks(ax, rotate=False)
ax.xaxis.set_visible(False)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="1%", pad=0.1, aspect=6)
plt.colorbar(im, cax=cax)
insul_region = bioframe.select(insulation_table, region)
ins_ax = divider.append_axes("bottom", size="50%", pad=0., sharex=ax)
ins_ax.set_prop_cycle(plt.cycler("color", plt.cm.plasma(np.linspace(0,1,5))))
ins_ax.plot(insul_region[['start', 'end']].mean(axis=1),
insul_region['log2_insulation_score_'+str(windows[0])],
label=f'Window {windows[0]} bp')
ins_ax.legend(bbox_to_anchor=(0., -1), loc='lower left', ncol=4);
format_ticks(ins_ax, y=False, rotate=False)
ax.set_xlim(region[1], region[2])
[7]:
(10500000.0, 13200000.0)
And now let’s add the other window sizes.
[8]:
for res in windows[1:]:
ins_ax.plot(insul_region[['start', 'end']].mean(axis=1), insul_region[f'log2_insulation_score_{res}'], label=f'Window {res} bp')
ins_ax.legend(bbox_to_anchor=(0., -1), loc='lower left', ncol=4);
f
[8]:
This really highlights how much the result is dependent on window size: smaller windows are sensitive to local structure, whereas large windows capture regions that insulate at larger scales.
Boundary calling
The insulation table also has annotations for valleys of the insulation score, which correspond to highly insulating regions, such as TAD boundaries. All potential boundaries have an assigned boundary_strength_ column. Additionally, this strength is thresholded to find regions that insulate particularly strongly, and this is recorded in the is_boundary_ columns.
Let’s repeat the previous plot and show where we found the boundaries:
[9]:
f, ax = plt.subplots(figsize=(20, 10))
im = pcolormesh_45deg(ax, data, start=region[1], resolution=resolution, norm=norm, cmap='fall')
ax.set_aspect(0.5)
ax.set_ylim(0, 10*windows[0])
format_ticks(ax, rotate=False)
ax.xaxis.set_visible(False)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="1%", pad=0.1, aspect=6)
plt.colorbar(im, cax=cax)
insul_region = bioframe.select(insulation_table, region)
ins_ax = divider.append_axes("bottom", size="50%", pad=0., sharex=ax)
ins_ax.plot(insul_region[['start', 'end']].mean(axis=1),
insul_region[f'log2_insulation_score_{windows[0]}'], label=f'Window {windows[0]} bp')
boundaries = insul_region[~np.isnan(insul_region[f'boundary_strength_{windows[0]}'])]
weak_boundaries = boundaries[~boundaries[f'is_boundary_{windows[0]}']]
strong_boundaries = boundaries[boundaries[f'is_boundary_{windows[0]}']]
ins_ax.scatter(weak_boundaries[['start', 'end']].mean(axis=1),
weak_boundaries[f'log2_insulation_score_{windows[0]}'], label='Weak boundaries')
ins_ax.scatter(strong_boundaries[['start', 'end']].mean(axis=1),
strong_boundaries[f'log2_insulation_score_{windows[0]}'], label='Strong boundaries')
ins_ax.legend(bbox_to_anchor=(0., -1), loc='lower left', ncol=4);
format_ticks(ins_ax, y=False, rotate=False)
ax.set_xlim(region[1], region[2])
[9]:
(10500000.0, 13200000.0)
Calculating boundary strength
Let’s inspect the histogram of boundary strengths to show how we selected the strong boundaries.
First, boundary strength is calculated using the peak prominence, on the dips (or minima) of the insulation profile.
[10]:
histkwargs = dict(
bins=10**np.linspace(-4,1,200),
histtype='step',
lw=2,
)
f, axs = plt.subplots(len(windows),1, sharex=True, figsize=(6,6), constrained_layout=True)
for i, (w, ax) in enumerate(zip(windows, axs)):
ax.hist(
insulation_table[f'boundary_strength_{w}'],
**histkwargs
)
ax.text(0.02, 0.9,
f'Window {w//1000}kb',
ha='left',
va='top',
transform=ax.transAxes)
ax.set(
xscale='log',
ylabel='# boundaries'
)
axs[-1].set(xlabel='Boundary strength');
As a quick way to automatically threshold the histogram, we borrow the tresholding methods from the image analysis field. These include Li (default threshold="Li") or Otsu, as implemented in scikit-image. Otsu is more conservative, whereas Li is more permissive.
In practice these thresholds work well for a simple parameter-free method for mammalian interphase data, though should be double-checked for any individual dataset.
[11]:
from skimage.filters import threshold_li, threshold_otsu
f, axs = plt.subplots(len(windows), 1, sharex=True, figsize=(6,6), constrained_layout=True)
thresholds_li = {}
thresholds_otsu = {}
for i, (w, ax) in enumerate(zip(windows, axs)):
ax.hist(
insulation_table[f'boundary_strength_{w}'],
**histkwargs
)
thresholds_li[w] = threshold_li(insulation_table[f'boundary_strength_{w}'].dropna().values)
thresholds_otsu[w] = threshold_otsu(insulation_table[f'boundary_strength_{w}'].dropna().values)
n_boundaries_li = (insulation_table[f'boundary_strength_{w}'].dropna()>=thresholds_li[w]).sum()
n_boundaries_otsu = (insulation_table[f'boundary_strength_{w}'].dropna()>=thresholds_otsu[w]).sum()
ax.axvline(thresholds_li[w], c='green')
ax.axvline(thresholds_otsu[w], c='magenta')
ax.text(0.01, 0.9,
f'Window {w//1000}kb',
ha='left',
va='top',
transform=ax.transAxes)
ax.text(0.01, 0.7,
f'{n_boundaries_otsu} boundaries (Otsu)',
c='magenta',
ha='left',
va='top',
transform=ax.transAxes)
ax.text(0.01, 0.5,
f'{n_boundaries_li} boundaries (Li)',
c='green',
ha='left',
va='top',
transform=ax.transAxes)
ax.set(
xscale='log',
ylabel='# boundaries'
)
axs[-1].set(xlabel='Boundary strength')
[11]:
[Text(0.5, 0, 'Boundary strength')]
CTCF enrichment at boundaries
TAD boundaries are frequently associated with CTCF binding.
To quantify this, we can aggregate the ChIP-Seq singal around the boundaries, and compare enrichment of CTCF with boundary strength using pybbi (https://github.com/nvictus/pybbi). We provide a test bigWig file with CTCF enrichment over input for the same cell type as the Micro-C data.
We use the bbi.stackup() method with no binning to extract an array of average values for all boundary regions with 1 kbp flanks.
[12]:
# Download test data. The file size is 592 Mb, so the download might take a while:
ctcf_fc_file = cooltools.download_data("HFF_CTCF_fc", cache=True, data_dir=data_dir)
[13]:
import bbi
[14]:
is_boundary = np.any([
~insulation_table[f'boundary_strength_{w}'].isnull()
for w in windows],
axis=0)
boundaries = insulation_table[is_boundary]
boundaries.head()
[14]:
| chrom | start | end | region | is_bad_bin | log2_insulation_score_30000 | n_valid_pixels_30000 | log2_insulation_score_50000 | n_valid_pixels_50000 | log2_insulation_score_100000 | ... | log2_insulation_score_250000 | n_valid_pixels_250000 | boundary_strength_30000 | boundary_strength_50000 | boundary_strength_250000 | boundary_strength_100000 | is_boundary_30000 | is_boundary_50000 | is_boundary_100000 | is_boundary_250000 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5 | chr2 | 50000 | 60000 | chr2 | False | 0.089080 | 6.0 | 0.059578 | 22.0 | 0.586104 | ... | 1.211581 | 122.0 | NaN | 0.156397 | NaN | NaN | False | False | False | False |
| 6 | chr2 | 60000 | 70000 | chr2 | False | 0.036906 | 6.0 | 0.134037 | 22.0 | 0.547732 | ... | 1.161302 | 147.0 | 0.150452 | NaN | NaN | NaN | False | False | False | False |
| 7 | chr2 | 70000 | 80000 | chr2 | False | 0.062353 | 6.0 | 0.122444 | 22.0 | 0.479052 | ... | 1.092480 | 172.0 | NaN | 0.011593 | NaN | NaN | False | False | False | False |
| 9 | chr2 | 90000 | 100000 | chr2 | False | 0.049426 | 6.0 | 0.198381 | 22.0 | 0.377645 | ... | 0.972715 | 222.0 | 0.029686 | NaN | NaN | NaN | False | False | False | False |
| 11 | chr2 | 110000 | 120000 | chr2 | False | 0.095762 | 6.0 | 0.190455 | 22.0 | 0.320182 | ... | 0.867080 | 272.0 | NaN | 0.024922 | NaN | NaN | False | False | False | False |
5 rows × 21 columns
[15]:
# Calculate the average ChIP singal/input in the 3kb region around the boundary.
flank = 1000 # Length of flank to one side from the boundary, in basepairs
ctcf_chip_signal = bbi.stackup(
data_dir+'/test_CTCF.bigWig',
boundaries.chrom,
boundaries.start-flank,
boundaries.end+flank,
bins=1).flatten()
Real boundaries are often enriched in CTCF binding, and this can be used as a guide for thresholding the boundary strength. However note a small population of strong boundaries without CTCF binding.
[16]:
w=windows[0]
f, ax = plt.subplots()
ax.loglog(
boundaries[f'boundary_strength_{w}'],
ctcf_chip_signal,
'o',
markersize=1,
alpha=0.05
);
ax.set(
xlim=(1e-4,1e1),
ylim=(3e-2,3e1),
xlabel='Boundary strength',
ylabel='CTCF enrichment over input')
ax.axvline(thresholds_otsu[w], ls='--', color='magenta', label='Otsu threshold')
ax.axvline(thresholds_li[w], ls='--', color='green', label='Li threshold')
ax.legend()
[16]:
<matplotlib.legend.Legend at 0x1afd95dc0>
If we were interested specifically in boundaries with CTCF, we could threshold based on enrichment of CTCF ChIP-seq:
[17]:
histkwargs = dict(
bins=10**np.linspace(-4,1,200),
histtype='step',
lw=2,
)
f, ax = plt.subplots()
ax.set(xscale='log', xlabel='Boundary strength')
ax.hist(
boundaries[f'boundary_strength_{windows[0]}'][ctcf_chip_signal>=2],
label='CTCF Chip/Input ≥ 2.0',
**histkwargs
);
ax.hist(
boundaries[f'boundary_strength_{windows[0]}'][ctcf_chip_signal<2],
label='CTCF Chip/Input < 2.0',
**histkwargs
);
ax.hist(
boundaries[f'boundary_strength_{windows[0]}'],
label='all boundaries',
**histkwargs
);
ax.legend(loc='upper left')
[17]:
<matplotlib.legend.Legend at 0x1af14eac0>
1D pileup: CTCF enrichment at boundaries
Additionally, we can create 1D pileup plot of average CTCF enrichment.
First, create a collection of genomic regions of equal size, each centered at the position of the boundary.
Then, create a stackup of binned ChIP-Seq signal for these regions. It is based on the same test bigWig file with the CTCF ChIP-Seq log fold change over input.
Finally, create 1D pileup by averaging each stacked window.
[18]:
# Select the strict thresholded boundaries for one window size
top_boundaries = insulation_table[insulation_table[f'boundary_strength_{windows[1]}']>=thresholds_otsu[windows[1]]]
[19]:
# Create of the stackup, the flanks are +- 50 Kb, number of bins is 100 :
flank = 50000 # Length of flank to one side from the boundary, in basepairs
nbins = 100 # Number of bins to split the region
stackup = bbi.stackup(data_dir+'/test_CTCF.bigWig',
top_boundaries.chrom,
top_boundaries.start+resolution//2-flank,
top_boundaries.start+resolution//2+flank,
bins=nbins)
[20]:
f, ax = plt.subplots(figsize=[7,5])
ax.plot(np.nanmean(stackup, axis=0) )
ax.set(xticks=np.arange(0, nbins+1, 10),
xticklabels=(np.arange(0, nbins+1, 10)-nbins//2)*flank*2/nbins/1000,
xlabel='Distance from boundary, kbp',
ylabel='CTCF ChIP-Seq mean fold change over input');
Using adjacent boundaries to create a table of TADs
Calling TADs from Hi-C data poses a challenge, in part because domain structures vary greatly in their size, intensity, and can be nested. The number of called TADs varies substantially from tool to tool, and can depend on tool-specific parameters (Forcato, 2017). Below, we show an example of how adjacent boundaries calculated with cooltools can specify a set of intervals that could be analyzed as TADs, using bioframe.merge().
[41]:
def extract_TADs(insulation_table, is_boundary_col, max_TAD_length = 3_000_000):
tads = bioframe.merge(insulation_table[insulation_table[is_boundary_col] == False])
return tads[ (tads["end"] - tads["start"]) <= MAX_TAD_LENGTH].reset_index(drop=True)[['chrom','start','end']]
TADs_table = extract_TADs(insulation_table, f'is_boundary_{windows[0]}')
TADs_table.head()
[46]:
TADs_table
[46]:
| chrom | start | end | |
|---|---|---|---|
| 0 | chr2 | 0 | 200000 |
| 1 | chr2 | 210000 | 290000 |
| 2 | chr2 | 300000 | 670000 |
| 3 | chr2 | 680000 | 740000 |
| 4 | chr2 | 750000 | 950000 |
| ... | ... | ... | ... |
| 1693 | chr17 | 82460000 | 82640000 |
| 1694 | chr17 | 82650000 | 82760000 |
| 1695 | chr17 | 82770000 | 82960000 |
| 1696 | chr17 | 82970000 | 83080000 |
| 1697 | chr17 | 83090000 | 83257441 |
1698 rows × 3 columns
[50]:
# Visualizing the first 10 inter-boundary intervals (grey overay) v.s. Hi-C data
region = ('chr2', TADs_table.iloc[0].start, TADs_table.iloc[9].end)
norm = LogNorm(vmax=0.1, vmin=0.001)
data = clr.matrix(balance=True).fetch(region)
f, ax = plt.subplots(figsize=(18, 6))
im = pcolormesh_45deg(ax, data, start=region[1], resolution=resolution, norm=norm, cmap='fall')
ax.set_aspect(0.5)
ax.set_ylim(0, 13*windows[0])
format_ticks(ax, rotate=False)
ax.xaxis.set_visible(False)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="1%", pad=0.1, aspect=6)
plt.colorbar(im, cax=cax)
idx = 10
max_pos = TADs_table[:idx]['end'].max()/resolution
contact_matrix = np.zeros((int(max_pos), int(max_pos)))
contact_matrix[:] = np.nan
for _, row in TADs_table[:idx].iterrows():
contact_matrix[int(row['start']/resolution):int(row['end']/resolution), int(row['start']/resolution):int(row['end']/resolution)] = 1
contact_matrix[int(row['start']/resolution + 1):int(row['end']/resolution - 1), int(row['start']/resolution + 1):int(row['end']/resolution - 1)] = np.nan
im = pcolormesh_45deg(ax, contact_matrix, start=0, resolution=resolution, cmap='gray', vmax=1, vmin=-1, alpha=0.6)
plt.show()
This page was generated with nbsphinx from /home/docs/checkouts/readthedocs.org/user_builds/cooltools/checkouts/stable/docs/notebooks/insulation_and_boundaries.ipynb
Dots & focal enrichment
Welcome to the dot calling notebook!
Punctate pairwise peaks of enriched contact frequency are a prevalent feature of mammalian interphase contact maps. These features are also referred to as ‘dots’ or ‘loops’ in the literature, and can appear either in isolation or as parts of grids and at the corners of domains.
HiCCUPS, proposed in Rao et al. 2014, is a common approach for calling dots in contact maps. HICCUPS uses a multi-step procedure to score and return a filtered list of extracted dots. Scoring is done by convolving a set of kernels with the contact map. However, since HICCUPS is written in Java it is challenging to modify the parameters used at specific steps of the calling procedure, which can be important for calling dots at new resolutions or in new organismal or cellular contexts.
Cooltools implements a similar approach for calling dots in Python. This enables users to easily vary the parameters and processing steps used for different Hi-C or Micro-C datasets.
[1]:
import pandas as pd
import numpy as np
from itertools import chain
# Hi-C utilities imports:
import cooler
import bioframe
import cooltools
from cooltools.lib.numutils import fill_diag
from packaging import version
if version.parse(cooltools.__version__) < version.parse('0.5.2'):
raise AssertionError("tutorials rely on cooltools version 0.5.2 or higher,"+
"please check your cooltools version and update to the latest")
# Visualization imports:
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import matplotlib.patches as patches
from matplotlib.ticker import EngFormatter
# helper functions for plotting
bp_formatter = EngFormatter('b')
def format_ticks(ax, x=True, y=True, rotate=True):
"""format ticks with genomic coordinates as human readable"""
if y:
ax.yaxis.set_major_formatter(bp_formatter)
if x:
ax.xaxis.set_major_formatter(bp_formatter)
ax.xaxis.tick_bottom()
if rotate:
ax.tick_params(axis='x',rotation=45)
Load data and define a genomic view
To call dots, we need an input cooler file with Hi-C data, and regions for calculation of expected (e.g. chromosomes or chromosome arms).
[2]:
# Download the test data from osf and define cooler:
data_dir = './data/'
cool_file = cooltools.download_data("HFF_MicroC", cache=True, data_dir=data_dir)
# 10 kb is a resolution at which one can clearly see "dots":
binsize = 10_000
# Open cool file with Micro-C data:
clr = cooler.Cooler(f'{data_dir}/test.mcool::/resolutions/{binsize}')
[3]:
# define genomic view that will be used to call dots and pre-compute expected
# Use bioframe to fetch the genomic features from the UCSC.
hg38_chromsizes = bioframe.fetch_chromsizes('hg38')
hg38_cens = bioframe.fetch_centromeres('hg38')
hg38_arms = bioframe.make_chromarms(hg38_chromsizes, hg38_cens)
# Select only chromosomes that are present in the cooler.
hg38_arms = hg38_arms.set_index("chrom").loc[clr.chromnames].reset_index()
# intra-arm expected
expected = cooltools.expected_cis(
clr,
view_df=hg38_arms,
nproc=4,
)
Dot-calling with default parameters
We first call dots with default parameters (i.e. similar to HiCCUPs). Later we illustrate the various parameters than can be easily modified in cooltools.
Here is a brief description of the steps involved in cooltools dots():
A set of convolution kernels are recommended based on the resolution of
clr, if user-defined convolution kernels are not provided (i.e.kernels=None).The requested portion of the heatmap (defined by
view_dfandmax_loci_separation) is split into smaller tiles of sizetile_size. This ensures the entire heatmap is not loaded into memory at once, and computationally intensive steps can be done in parallel usingnprocworkers.tile_sizeandnprocdo not affect the outcome of the procedure.Tiles of the heatmap are convolved with the provided kernels to calculate localy adjusted expected for each pixel. This is in turn used to calculate p-values, assuming a Poisson distribution of pixel counts.
Pixels are assigned to geometrically-spaced “lambda-bins” of locally-adjusted expected for statistical testing. Within each lambda-bin, signficantly enriched pixels are “caled” using BH-FDR multiple hypothesis testing procedure, and thresholds of significance are calculated for each lambda-bin and each kernel-type (controlled by
lambda_bin_fdr).Significantly-enriched pixels are extracted, based on the thresholds in each lambda bin. Note the cooltools implementation of this step involves a second pass with the same convolution kernels to re-score pixels, as this is less costly than storing all such scores in memory.
Additional clustering and empirical filtering is optionally performed (depending on
clustering_radiusandcluster_filtering).
See the `dotfinder docstring <https://github.com/open2c/cooltools/blob/master/cooltools/api/dotfinder.py>`__ for additional practical details of the implementation.
[4]:
dots_df = cooltools.dots(
clr,
expected=expected,
view_df=hg38_arms,
# how far from the main diagonal to call dots:
max_loci_separation=10_000_000,
nproc=4,
)
INFO:root:Using recommended donut-based kernels with w=5, p=2 for binsize=10000
INFO:root: matrix 9314X9314 to be split into 361 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 14907X14907 to be split into 900 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 2472X2472 to be split into 25 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 5855X5855 to be split into 144 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root:convolving 186 tiles to build histograms for lambda-bins
INFO:root:creating a Pool of 4 workers to tackle 186 tiles
INFO:root:Done building histograms in 29.498 sec ...
INFO:root:Determined thresholds for every lambda-bin ...
INFO:root:convolving 186 tiles to extract enriched pixels
INFO:root:creating a Pool of 4 workers to tackle 186 tiles
INFO:root:Done extracting enriched pixels in 22.276 sec ...
INFO:root:Begin post-processing of 15303 filtered pixels
INFO:root:preparing to extract needed q-values ...
INFO:root:clustering enriched pixels in region: chr17_p
INFO:root:detected 341 clusters of 2.96+/-2.60 size
INFO:root:clustering enriched pixels in region: chr17_q
INFO:root:detected 939 clusters of 3.23+/-2.99 size
INFO:root:clustering enriched pixels in region: chr2_p
INFO:root:detected 1400 clusters of 3.12+/-2.93 size
INFO:root:clustering enriched pixels in region: chr2_q
INFO:root:detected 2203 clusters of 3.13+/-2.87 size
INFO:root:Clustering is complete
INFO:root:filtered 3145 out of 4883 centroids to reduce the number of false-positives
Visualizing dot-calling with the default parameters
To visualize the results of this dot calling, we overlay small rectangles at the positions of the called dots over the HiC map.
[5]:
# create a functions that would return a series of rectangles around called dots
# in a specific region, and exposing importnat plotting parameters
def rectangles_around_dots(dots_df, region, loc="upper", lw=1, ec="cyan", fc="none"):
"""
yield a series of rectangles around called dots in a given region
"""
# select dots from the region:
df_reg = bioframe.select(
bioframe.select(dots_df, region, cols=("chrom1","start1","end1")),
region,
cols=("chrom2","start2","end2"),
)
rectangle_kwargs = dict(lw=lw, ec=ec, fc=fc)
# draw rectangular "boxes" around pixels called as dots in the "region":
for s1, s2, e1, e2 in df_reg[["start1", "start2", "end1", "end2"]].itertuples(index=False):
width1 = e1 - s1
width2 = e2 - s2
if loc == "upper":
yield patches.Rectangle((s2, s1), width2, width1, **rectangle_kwargs)
elif loc == "lower":
yield patches.Rectangle((s1, s2), width1, width2, **rectangle_kwargs)
else:
raise ValueError("loc has to be uppper or lower")
[6]:
# define a region to look into as an example
start = 34_150_000
end = start + 1_200_000
region = ('chr17', start, end)
# heatmap kwargs
matshow_kwargs = dict(
cmap='YlOrBr',
norm=LogNorm(vmax=0.05),
extent=(start, end, end, start)
)
# colorbar kwargs
colorbar_kwargs = dict(fraction=0.046, label='corrected frequencies')
# compute heatmap for the region
region_matrix = clr.matrix(balance=True).fetch(region)
for diag in [-1,0,1]:
region_matrix = fill_diag(region_matrix, np.nan, i=diag)
# see viz.ipynb for details of heatmap visualization
f, ax = plt.subplots(figsize=(7,7))
im = ax.matshow( region_matrix, **matshow_kwargs)
format_ticks(ax, rotate=False)
plt.colorbar(im, ax=ax, **colorbar_kwargs)
# draw rectangular "boxes" around pixels called as dots in the "region":
for box in rectangles_around_dots(dots_df, region, lw=1.5):
ax.add_patch(box)
Skipping clustering and cluster enrichment filtering
Dot-calling returns pixels that are enriched relative to some local background. Such pixels often come in groups (“clusters”). By default dots() picks a single representative for each cluster (i.e. centroid). However, cooltools users can easily turn clustering off for debugging or alternative clustering approaches:
[7]:
dots_df_all = cooltools.dots(
clr,
expected=expected,
view_df=hg38_arms,
max_loci_separation=10_000_000,
clustering_radius=None, # None - implies no clustering
cluster_filtering=False, # ignored when clustering is off
nproc=4,
)
INFO:root:Using recommended donut-based kernels with w=5, p=2 for binsize=10000
INFO:root: matrix 9314X9314 to be split into 361 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 14907X14907 to be split into 900 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 2472X2472 to be split into 25 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 5855X5855 to be split into 144 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root:convolving 186 tiles to build histograms for lambda-bins
INFO:root:creating a Pool of 4 workers to tackle 186 tiles
INFO:root:Done building histograms in 25.523 sec ...
INFO:root:Determined thresholds for every lambda-bin ...
INFO:root:convolving 186 tiles to extract enriched pixels
INFO:root:creating a Pool of 4 workers to tackle 186 tiles
INFO:root:Done extracting enriched pixels in 23.327 sec ...
INFO:root:Begin post-processing of 15303 filtered pixels
INFO:root:preparing to extract needed q-values ...
The visualization below compares clustered dots (cyan) with all enriched pixels before clustering (blue)
[8]:
f, ax = plt.subplots(figsize=(7,7))
# draw heatmap
im = ax.matshow(region_matrix, **matshow_kwargs)
format_ticks(ax, rotate=False)
plt.colorbar(im, ax=ax, **colorbar_kwargs)
# draw rectangular "boxes" around pixels called as dots in the "region":
for rect in chain(
rectangles_around_dots(dots_df, region, lw=1.5), # clustered & filtered
rectangles_around_dots(dots_df_all, region, loc="lower", ec="blue"), # unclustered
):
ax.add_patch(rect)
Convolution kernels and local expected
A useful local background to calculate the enrichment of pixels was defined in Rao et al. 2014 as a “donut”-shaped surrounding of a given pixel between ~20 to ~50 kb away from that pixel.
Such a local surrounding is best thought of in the terms of convolutional kernels e.g. as in image processing. In this framework, calcluating the local background for all pixels is simply obtained as the convolution of a contact map with the “donut”-shaped kernel.
Additional kernels can be used to downweight unwanted enrichment types. In addition to the “donut” kernel, the default kernels recommended in cooltools dots() are: - “vertical” to avoid calling pixels that are part of vertical stripes as dots - “horizontal” to avoid calling pixels that are part of horizontal stripes as dots - “lowleft” to avoid calling pixels at the corners of domains as dots
These four kernels are illustrated below, where pixels that are included in the calculations are highlighted in yellow, the pixel of interest is highlighted in red, and pixels that are not included in the local background are in purple. A checkerboard pattern is overlayed on the figure to emphasize individual pixels.
[9]:
# function to draw kernels:
def draw_kernel(kernel, axis=None, cmap='viridis'):
if axis is None:
f, axis = plt.subplots()
# kernel:
imk = axis.imshow(
kernel[::-1,::-1], # flip it, as in convolution
alpha=0.85,
cmap=cmap,
interpolation='nearest')
# draw a square around the target pixel:
x0 = kernel.shape[0] // 2 - 0.5
y0 = kernel.shape[1] // 2 - 0.5
rect = patches.Rectangle((x0, y0), 1, 1, lw=1, ec='r', fc='r')
axis.add_patch(rect)
# clean axis:
axis.set_xticks([])
axis.set_yticks([])
axis.set_xticklabels('',visible=False)
axis.set_yticklabels('',visible=False)
axis.set_title("{} kernel".format(ktype),fontsize=16)
# add a checkerboard to highlight pixels:
checkerboard = np.add.outer(range(kernel.shape[0]),
range(kernel.shape[1])) % 2
# show it:
axis.imshow(checkerboard,
cmap='gray',
interpolation='nearest',
alpha=0.3)
return imk
[10]:
kernels = cooltools.api.dotfinder.recommend_kernels(binsize)
fig, axs = plt.subplots(ncols=4, figsize=(12,2.5))
for ax, (ktype, kernel) in zip(axs, kernels.items()):
imk = draw_kernel(kernel, ax)
INFO:root:Using recommended donut-based kernels with w=5, p=2 for binsize=10000
Calling dots with a “rounded donut” kernel
Cooltools enables experimentation and modification of kernels used for determining local enrichment scores. Here we show the result for replacing the default “donut” kernel with a “rounded donut”.
[11]:
# create a grid of coordinates from -5 to 5, to define round kernels
# see https://numpy.org/doc/stable/reference/generated/numpy.meshgrid.html for details
half = 5 # half width of the kernel
x, y = np.meshgrid(
np.linspace(-half, half, 2*half + 1),
np.linspace(-half, half, 2*half + 1),
)
# now define a donut-like mask as pixels between 2 radii: sqrt(7) and sqrt(30):
mask = (x**2+y**2 > 7) & (x**2+y**2 <= 30)
mask[:,half] = 0
mask[half,:] = 0
# lowleft mask - zero out neccessary parts
mask_ll = mask.copy()
mask_ll[:,:half] = 0
mask_ll[half:,:] = 0
# new kernels with more round donut and lowleft masks:
kernels_round = {'donut': mask,
'vertical': kernels["vertical"].copy(),
'horizontal': kernels["horizontal"].copy(),
'lowleft': mask_ll}
# plot rounded kernels
fig, axs = plt.subplots(ncols=4, figsize=(12,2.5))
for ax, (ktype, kernel) in zip(axs, kernels_round.items()):
imk = draw_kernel(kernel, ax)
[12]:
#### call dots using redefined kernels (without clustering)
dots_round_df_all = cooltools.dots(
clr,
expected=expected,
view_df=hg38_arms,
kernels=kernels_round, # provide custom kernels
max_loci_separation=10_000_000,
clustering_radius=None,
nproc=4,
)
/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/cooltools/api/dotfinder.py:1571: UserWarning: Compatibility checks for 'kernels' are not fully implemented yet, use at your own risk
warnings.warn(
INFO:root: matrix 9314X9314 to be split into 361 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 14907X14907 to be split into 900 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 2472X2472 to be split into 25 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 5855X5855 to be split into 144 tiles of 500X500.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root:convolving 186 tiles to build histograms for lambda-bins
INFO:root:creating a Pool of 4 workers to tackle 186 tiles
INFO:root:Done building histograms in 33.029 sec ...
INFO:root:Determined thresholds for every lambda-bin ...
INFO:root:convolving 186 tiles to extract enriched pixels
INFO:root:creating a Pool of 4 workers to tackle 186 tiles
INFO:root:Done extracting enriched pixels in 23.135 sec ...
INFO:root:Begin post-processing of 16716 filtered pixels
INFO:root:preparing to extract needed q-values ...
The visualization below compares dots called using “rounded” kernels (cyan) with the dots called using recommended kernels (blue). As one can tell the results are similar, yet the “rounded” kernels allow for calling dots closer to the diagonal because of the shape of the kernel.
[13]:
f, ax = plt.subplots(figsize=(7,7))
# draw heatmap
im = ax.matshow(region_matrix, **matshow_kwargs)
format_ticks(ax, rotate=False)
plt.colorbar(im, ax=ax, **colorbar_kwargs)
# draw rectangular "boxes" around pixels called as dots in the "region":
for rect in chain(
rectangles_around_dots(dots_round_df_all, region),
rectangles_around_dots(dots_df_all, region, loc="lower", ec="blue"),
):
ax.add_patch(rect)
[14]:
# TODO CTCF-based analysis to look
This page was generated with nbsphinx from /home/docs/checkouts/readthedocs.org/user_builds/cooltools/checkouts/stable/docs/notebooks/dots.ipynb
Pileups and average features
Welcome to the cooltools pileups notebook!
Averaging Hi-C/Micro-C maps allows the quantification of general patterns observed in the maps. Averaging comes in various forms: contact-vs-distance plots, saddle plots, and pileup plots. Pileup plots are the averaged local Hi-C map over the 2D windows (i.e. snippets). These are also referred to as “average Hi-C maps”. Pileups can be useful for determining the relationship between features (e.g. CTCF and TAD boundaries). Pileups can also be beneficial for reliably observing features in low-coverage Hi-C or single-cell HiC maps.
For pileups, we retrieve local windows that are centered at the anchors. We call this procedure snipping. Anchors can be ChIP-Seq binding sites, anchors of dots, or any other genomic features. Pileups come in two varieties:
On-diagonal pileup. Each window is centered at the pixel located at the anchor position, at the main diagonal. Both coordinates of the window center are equivalent to the bin of the anchor.
Off-diagonal pileup. Each window is centered at the pixel with one anchor as a left coordinate and another anchor as a right coordinate.
Typically, the sizes of windows are equivalent. After the selection of windows, we average them elementwise.
Content:
Download data
Load data
Load genomic regions
Load features for anchors
On-diagonal pipeup of CTCF
On-diagonal pileup of ICed Hi-C interactions
On-diagonal pileup of observed over expected interactions
Inspect the snips
Off-diagonal pileup of CTCF
[1]:
# If you are a developer, you may want to reload the packages on a fly.
# Jupyter has a magic for this particular purpose:
%load_ext autoreload
%autoreload 2
[2]:
# import standard python libraries
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
[3]:
# import libraries for biological data analysis
import cooler
import bioframe
import cooltools
from packaging import version
if version.parse(cooltools.__version__) < version.parse('0.5.2'):
raise AssertionError("tutorials rely on cooltools version 0.5.2 or higher,"+
"please check your cooltools version and update to the latest")
Download data
For this example notebook, we collected the data from immortalized human foreskin fibroblast cell line HFFc6:
Micro-C data from Krietenstein et al. 2020
ChIP-Seq for CTCF from ENCODE ENCSR000DWQ
You can automatically download test datasets with cooltools. More information on the files and how they were obtained is available from the datasets description.
[4]:
# Print available datasets for download
cooltools.print_available_datasets()
1) HFF_MicroC : Micro-C data from HFF human cells for two chromosomes (hg38) in a multi-resolution mcool format.
Downloaded from https://osf.io/3h9js/download
Stored as test.mcool
Original md5sum: e4a0fc25c8dc3d38e9065fd74c565dd1
2) HFF_CTCF_fc : ChIP-Seq fold change over input with CTCF antibodies in HFF cells (hg38). Downloaded from ENCODE ENCSR000DWQ, ENCFF761RHS.bigWig file
Downloaded from https://osf.io/w92u3/download
Stored as test_CTCF.bigWig
Original md5sum: 62429de974b5b4a379578cc85adc65a3
3) HFF_CTCF_binding : Binding sites called from CTCF ChIP-Seq peaks for HFF cells (hg38). Peaks are from ENCODE ENCSR000DWQ, ENCFF498QCT.bed file. The motifs are called with gimmemotifs (options --nreport 1 --cutoff 0), with JASPAR pwm MA0139.
Downloaded from https://osf.io/c9pwe/download
Stored as test_CTCF.bed.gz
Original md5sum: 61ecfdfa821571a8e0ea362e8fd48f63
[5]:
# Downloading test data for pileups
# cache = True will doanload the data only if it was not previously downloaded
data_dir = './data/'
cool_file = cooltools.download_data("HFF_MicroC", cache=True, data_dir=data_dir)
ctcf_peaks_file = cooltools.download_data("HFF_CTCF_binding", cache=True, data_dir=data_dir)
ctcf_fc_file = cooltools.download_data("HFF_CTCF_fc", cache=True, data_dir=data_dir)
Load data
Load genomic regions
The pileup function needs genomic regions. Why?
First, pileup uses regions for parallelization of snipping. Different genomic regions are loaded simultaneously by different processes, and the snipping can be done in parallel.
Second, the observed over expected pileup requires calculating expected interactions before snipping (P(s), in other words). Typically, P(s) is calculated separately for each chromosome arm as inter-arms interactions might be affected by strong insulation of centromeres or Rabl configuration.
For species that do not have information on chromosome arms, or have telocentric chromosomes (e.g., mouse), you may want to use full chromosomes instead.
[6]:
# Open cool file with Micro-C data:
clr = cooler.Cooler(data_dir+'/test.mcool::/resolutions/10000')
# Set up selected data resolution:
resolution = clr.binsize
[7]:
# Use bioframe to fetch the genomic features from the UCSC.
hg38_chromsizes = bioframe.fetch_chromsizes('hg38')
hg38_cens = bioframe.fetch_centromeres('hg38')
hg38_arms = bioframe.make_chromarms(hg38_chromsizes, hg38_cens)
# Select only chromosomes that are present in the cooler.
# This step is typically not required! we call it only because the test data are reduced.
hg38_arms = hg38_arms.set_index("chrom").loc[clr.chromnames].reset_index()
Load features for anchors
Construction of the pileup requires genomic features that will be used for centering of the snippets. In this example, we will use positions of motifs in CTCF peaks as features.
[8]:
# Read CTCF peaks data and select only chromosomes present in cooler:
ctcf = bioframe.read_table(ctcf_peaks_file, schema='bed').query(f'chrom in {clr.chromnames}')
ctcf['mid'] = (ctcf.end+ctcf.start)//2
ctcf.head()
[8]:
| chrom | start | end | name | score | strand | mid | |
|---|---|---|---|---|---|---|---|
| 17271 | chr17 | 118485 | 118504 | MA0139.1_CTCF_human | 12.384042 | - | 118494 |
| 17272 | chr17 | 144002 | 144021 | MA0139.1_CTCF_human | 11.542617 | + | 144011 |
| 17273 | chr17 | 163676 | 163695 | MA0139.1_CTCF_human | 5.294219 | - | 163685 |
| 17274 | chr17 | 164711 | 164730 | MA0139.1_CTCF_human | 11.889376 | + | 164720 |
| 17275 | chr17 | 309416 | 309435 | MA0139.1_CTCF_human | 7.879575 | - | 309425 |
Since we have both the list of strongest motifs of CTCF located in CTCF ChIP-Seq and the fold change over input for the genome, we have two characteristics of each feature:
score of the motif
CTCF ChIP-Seq fold-change over input
Let’s take a look at joint distribution of these scores:
[9]:
import bbi
from scipy.stats import linregress
[10]:
# Get CTCF ChIP-Seq fold-change over input for genomic regions centered at the positions of the motifs
flank = 250 # Length of flank to one side from the boundary, in basepairs
ctcf_chip_signal = bbi.stackup(
ctcf_fc_file,
ctcf.chrom,
ctcf.mid-flank,
ctcf.mid+flank,
bins=1)
ctcf['FC_score'] = ctcf_chip_signal
[11]:
ctcf['quartile_score'] = pd.qcut(ctcf['score'], 4, labels=False) + 1
ctcf['quartile_FC_score'] = pd.qcut(ctcf['FC_score'], 4, labels=False) + 1
ctcf['peaks_importance'] = ctcf.apply(
lambda x: 'Top by both scores' if x.quartile_score==4 and x.quartile_FC_score==4 else
'Top by Motif score' if x.quartile_score==4 else
'Top by FC score' if x.quartile_FC_score==4 else 'Ordinary peaks', axis=1
)
[12]:
x = ctcf['score']
y = np.log(ctcf['FC_score'])
fig, ax = plt.subplots()
sns.scatterplot(x=x, y=y, hue=ctcf['peaks_importance'],
s=2,
alpha=0.5,
label='All peaks',
ax=ax
)
slope, intercept, r, p, se = linregress(x, y)
ax.plot([-6, 19], [intercept-6*slope, intercept+19*slope],
alpha=0.5,
color='black',
label=f"Regression line, R value: {r:.2f}")
ax.set(
xlabel='Motif score',
ylabel='ChIP-Seq fold-change over input')
ax.legend(bbox_to_anchor=(1.01,1), loc="upper left")
plt.show()
/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.8/site-packages/seaborn/_decorators.py:36: FutureWarning: Pass the following variables as keyword args: x, y. From version 0.12, the only valid positional argument will be `data`, and passing other arguments without an explicit keyword will result in an error or misinterpretation.
warnings.warn(
[13]:
# Select the CTCF sites that are in top quartile by both the ChIP-Seq data and motif score
sites = ctcf[ctcf['peaks_importance']=='Top by both scores']\
.sort_values('FC_score', ascending=False)\
.reset_index(drop=True)
sites.tail()
[13]:
| chrom | start | end | name | score | strand | mid | FC_score | quartile_score | quartile_FC_score | peaks_importance | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 659 | chr17 | 8158938 | 8158957 | MA0139.1_CTCF_human | 13.276979 | - | 8158947 | 25.056849 | 4 | 4 | Top by both scores |
| 660 | chr2 | 176127201 | 176127220 | MA0139.1_CTCF_human | 12.820343 | + | 176127210 | 25.027294 | 4 | 4 | Top by both scores |
| 661 | chr17 | 38322364 | 38322383 | MA0139.1_CTCF_human | 13.534864 | - | 38322373 | 25.010430 | 4 | 4 | Top by both scores |
| 662 | chr2 | 119265336 | 119265355 | MA0139.1_CTCF_human | 13.739862 | - | 119265345 | 24.980141 | 4 | 4 | Top by both scores |
| 663 | chr2 | 118003514 | 118003533 | MA0139.1_CTCF_human | 12.646685 | - | 118003523 | 24.957502 | 4 | 4 | Top by both scores |
[14]:
# Some CTCF sites might be located too close in the genome and interfere with analysis.
# We will collapse the sites falling into the same size genomic bins as the resolution of our micro-C data:
sites = bioframe.cluster(sites, min_dist=resolution)\
.drop_duplicates('cluster')\
.reset_index(drop=True)
sites.tail()
[14]:
| chrom | start | end | name | score | strand | mid | FC_score | quartile_score | quartile_FC_score | peaks_importance | cluster | cluster_start | cluster_end | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 608 | chr17 | 8158938 | 8158957 | MA0139.1_CTCF_human | 13.276979 | - | 8158947 | 25.056849 | 4 | 4 | Top by both scores | 34 | 8158938 | 8158957 |
| 609 | chr2 | 176127201 | 176127220 | MA0139.1_CTCF_human | 12.820343 | + | 176127210 | 25.027294 | 4 | 4 | Top by both scores | 515 | 176127201 | 176127220 |
| 610 | chr17 | 38322364 | 38322383 | MA0139.1_CTCF_human | 13.534864 | - | 38322373 | 25.010430 | 4 | 4 | Top by both scores | 104 | 38322364 | 38322383 |
| 611 | chr2 | 119265336 | 119265355 | MA0139.1_CTCF_human | 13.739862 | - | 119265345 | 24.980141 | 4 | 4 | Top by both scores | 465 | 119265336 | 119265355 |
| 612 | chr2 | 118003514 | 118003533 | MA0139.1_CTCF_human | 12.646685 | - | 118003523 | 24.957502 | 4 | 4 | Top by both scores | 462 | 118003514 | 118003533 |
On-diagonal pileup
On-diagonal pileup is the simplest, you need the positions of features (middlepoints of CTCF motifs) and the size of flanks aroung each motif. cooltools will create a snippet of Hi-C map for each feature. Then you can combine them into a single 2D pileup.
On-diagonal pileup of ICed Hi-C interactions
[15]:
stack = cooltools.pileup(clr, sites, view_df=hg38_arms, flank=300_000)
# Mirror reflect snippets when the feature is on the opposite strand
mask = np.array(sites.strand == '-', dtype=bool)
stack[:, :, mask] = stack[::-1, ::-1, mask]
# Aggregate. Note that some pixels might be converted to NaNs after IC, thus we aggregate by nanmean:
mtx = np.nanmean(stack, axis=2)
[16]:
# Load colormap with large number of distinguishable intermediary tones,
# The "fall" colormap in cooltools is exactly for this purpose.
# After this step, you can use "fall" as cmap parameter in matplotlib:
import cooltools.lib.plotting
[17]:
plt.imshow(
np.log10(mtx),
vmin = -3,
vmax = -1,
cmap='fall',
interpolation='none')
plt.colorbar(label = 'log10 mean ICed Hi-C')
ticks_pixels = np.linspace(0, flank*2//resolution,5)
ticks_kbp = ((ticks_pixels-ticks_pixels[-1]/2)*resolution//1000).astype(int)
plt.xticks(ticks_pixels, ticks_kbp)
plt.yticks(ticks_pixels, ticks_kbp)
plt.xlabel('relative position, kbp')
plt.ylabel('relative position, kbp')
plt.show()
/var/folders/4s/d866wm3s4zbc9m41334fxfwr0000gp/T/ipykernel_33615/2426526626.py:2: RuntimeWarning: divide by zero encountered in log10
np.log10(mtx),
On-diagonal pileup of observed over expected interactions
Sometimes you don’t want to include the distance decay P(s) in your pileups. For example, when you make comparison of pileups between experiments and they have different P(s). Even if these differences are slight, they might affect the pileup of raw ICed Hi-C interactions.
In this case, the observed over expected pileup is your choice. Prior to running the pileup function, you need to calculate expected interactions for chromosome arms.
[18]:
expected = cooltools.expected_cis(clr, view_df=hg38_arms, nproc=2, chunksize=1_000_000)
[19]:
expected
[19]:
| region1 | region2 | dist | n_valid | count.sum | balanced.sum | count.avg | balanced.avg | balanced.avg.smoothed | balanced.avg.smoothed.agg | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr2_p | chr2_p | 0 | 8771 | NaN | NaN | NaN | NaN | NaN | NaN |
| 1 | chr2_p | chr2_p | 1 | 8753 | NaN | NaN | NaN | NaN | 0.000495 | 0.000520 |
| 2 | chr2_p | chr2_p | 2 | 8745 | 2656738.0 | 406.013088 | 303.800800 | 0.046428 | 0.042469 | 0.044728 |
| 3 | chr2_p | chr2_p | 3 | 8741 | 1563363.0 | 237.585271 | 178.854021 | 0.027181 | 0.026796 | 0.028226 |
| 4 | chr2_p | chr2_p | 4 | 8738 | 1125674.0 | 169.308714 | 128.825132 | 0.019376 | 0.019097 | 0.020152 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 32543 | chr17_q | chr17_q | 5850 | 0 | 0.0 | 0.000000 | NaN | NaN | 0.000010 | 0.000006 |
| 32544 | chr17_q | chr17_q | 5851 | 0 | 0.0 | 0.000000 | NaN | NaN | 0.000010 | 0.000006 |
| 32545 | chr17_q | chr17_q | 5852 | 0 | 0.0 | 0.000000 | NaN | NaN | 0.000010 | 0.000006 |
| 32546 | chr17_q | chr17_q | 5853 | 0 | 0.0 | 0.000000 | NaN | NaN | 0.000010 | 0.000006 |
| 32547 | chr17_q | chr17_q | 5854 | 0 | 0.0 | 0.000000 | NaN | NaN | 0.000010 | 0.000006 |
32548 rows × 10 columns
[20]:
# Create the stack of snips:
stack = cooltools.pileup(clr, sites, view_df=hg38_arms, expected_df=expected, flank=300_000)
# Mirror reflect snippets when the feature is on the opposite strand
mask = np.array(sites.strand == '-', dtype=bool)
stack[:, :, mask] = stack[::-1, ::-1, mask]
mtx = np.nanmean(stack, axis=2)
[21]:
plt.imshow(
np.log2(mtx),
vmax = 1.0,
vmin = -1.0,
cmap='coolwarm',
interpolation='none')
plt.colorbar(label = 'log2 mean obs/exp')
ticks_pixels = np.linspace(0, flank*2//resolution,5)
ticks_kbp = ((ticks_pixels-ticks_pixels[-1]/2)*resolution//1000).astype(int)
plt.xticks(ticks_pixels, ticks_kbp)
plt.yticks(ticks_pixels, ticks_kbp)
plt.xlabel('relative position, kbp')
plt.ylabel('relative position, kbp')
plt.show()
/var/folders/4s/d866wm3s4zbc9m41334fxfwr0000gp/T/ipykernel_33615/2557000624.py:2: RuntimeWarning: divide by zero encountered in log2
np.log2(mtx),
Inspect the snips
Aggregation is a convenient though dangerous step. It averages your data so that you cannot distinguish whether the signal is indeed average, or there is a single dataset that introduces a bias to your analysis. To make sure there are no outliers, you may want to use inspection of individual snippets.
The cell below shows one way to interactively investigate snippets contributing to a pileup. Note that this is not interactive on readthedocs, but can be run if the notebook is obtained from open2c_examples. This widget sorts the dataframe with CTCF motifs by the strength of binding. This allows us to inspect the Micro-C maps at the positions of the strongest and weakest CTCF sites. Run the cell below and try to compare snippets with the lowest score to the snippets with the largest score.
[22]:
from ipywidgets import interact
from matplotlib.gridspec import GridSpec
n_examples = len(sites)
@interact(i=(0, n_examples-1))
def f(i):
fig, ax = plt.subplots(figsize=[5,5])
img = ax.matshow(
np.log2(stack[:, :, i]),
vmin=-1,
vmax=1,
extent=[-flank//1000, flank//1000, -flank//1000, flank//1000],
cmap='coolwarm'
)
ax.xaxis.tick_bottom()
if i > 0:
ax.yaxis.set_visible(False)
plt.title(f'{i+1}-th snippet from top \n FC score: {sites.loc[i, "FC_score"]:.2f}\n and motif score: {sites.loc[i, "score"]:.2f}')
plt.axvline(0, c='g', ls=':')
plt.axhline(0, c='g', ls=':')
Compare top strongest peaks with others
Compare the top peaks with both motif score and FC score to the rest of the peaks:
[23]:
# Create the stack of snips:
stack = cooltools.pileup(clr, ctcf, view_df=hg38_arms, expected_df=expected, flank=300_000
)
# Mirror reflect snippets where the feature is on the opposite strand
mask = np.array(ctcf.strand == '-', dtype=bool)
stack[:, :, mask] = stack[::-1, ::-1, mask]
mtx = np.nanmean(stack, axis=2)
[24]:
# TODO: add some strength of insulation for the pileup?
groups = ['Top by both scores', 'Ordinary peaks']
n_groups = len(groups)
ticks_pixels = np.linspace(0, flank*2//resolution,5)
ticks_kbp = ((ticks_pixels-ticks_pixels[-1]/2)*resolution//1000).astype(int)
fig, axs = plt.subplots(1, n_groups, sharex=True, sharey=True, figsize=(4*n_groups, 4))
for i in range(n_groups):
mtx = np.nanmean( stack[:, :, ctcf['peaks_importance']==groups[i]], axis=2)
ax = axs[i]
ax.imshow(
np.log2(mtx),
vmax = 1.0,
vmin = -1.0,
cmap='coolwarm',
interpolation='none')
ax.set(title=f'{groups[i]} group',
xticks=ticks_pixels,
xticklabels=ticks_kbp,
xlabel='relative position, kbp')
axs[0].set(yticks=ticks_pixels,
yticklabels=ticks_kbp,
ylabel='relative position, kbp')
plt.show()
/var/folders/4s/d866wm3s4zbc9m41334fxfwr0000gp/T/ipykernel_33615/2210978640.py:14: RuntimeWarning: divide by zero encountered in log2
np.log2(mtx),
Off-diagonal pileup
Off-diagonal pileups are the averaged Hi-C maps around double anchors. In this case, the anchors are CTCF sites in the genome.
[25]:
paired_sites = bioframe.pair_by_distance(sites, min_sep=200000, max_sep=1000000, suffixes=('1', '2'))
paired_sites.loc[:, 'mid1'] = (paired_sites['start1'] + paired_sites['end1'])//2
paired_sites.loc[:, 'mid2'] = (paired_sites['start2'] + paired_sites['end2'])//2
[26]:
print(len(paired_sites))
paired_sites.head()
1634
[26]:
| chrom1 | start1 | end1 | name1 | score1 | strand1 | mid1 | FC_score1 | quartile_score1 | quartile_FC_score1 | ... | score2 | strand2 | mid2 | FC_score2 | quartile_score2 | quartile_FC_score2 | peaks_importance2 | cluster2 | cluster_start2 | cluster_end2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr17 | 412407 | 412426 | MA0139.1_CTCF_human | 12.212548 | + | 412416 | 41.645123 | 4 | 4 | ... | 13.272118 | - | 1056231 | 35.072572 | 4 | 4 | Top by both scores | 1 | 1056222 | 1056241 |
| 1 | chr17 | 412407 | 412426 | MA0139.1_CTCF_human | 12.212548 | + | 412416 | 41.645123 | 4 | 4 | ... | 13.996208 | - | 1187374 | 69.994562 | 4 | 4 | Top by both scores | 2 | 1187365 | 1187384 |
| 2 | chr17 | 412407 | 412426 | MA0139.1_CTCF_human | 12.212548 | + | 412416 | 41.645123 | 4 | 4 | ... | 14.735101 | + | 1259280 | 31.643758 | 4 | 4 | Top by both scores | 3 | 1259271 | 1259290 |
| 3 | chr17 | 412407 | 412426 | MA0139.1_CTCF_human | 12.212548 | + | 412416 | 41.645123 | 4 | 4 | ... | 13.983562 | + | 1276338 | 35.440247 | 4 | 4 | Top by both scores | 4 | 1276329 | 1276348 |
| 4 | chr17 | 412407 | 412426 | MA0139.1_CTCF_human | 12.212548 | + | 412416 | 41.645123 | 4 | 4 | ... | 12.045221 | + | 1365609 | 36.746886 | 4 | 4 | Top by both scores | 5 | 1365600 | 1365619 |
5 rows × 28 columns
For pileup, we will use the expected calculated above:
[27]:
# create the stack of snips:
stack = cooltools.pileup(clr, paired_sites, view_df=hg38_arms, expected_df=expected, flank=100_000)
mtx = np.nanmean(stack, axis=2)
[28]:
plt.imshow(
np.log2(mtx),
vmax = 1,
vmin = -1,
cmap='coolwarm')
plt.colorbar(label = 'log2 mean obs/exp')
ticks_pixels = np.linspace(0, flank*2//resolution,5)
ticks_kbp = ((ticks_pixels-ticks_pixels[-1]/2)*resolution//1000).astype(int)
plt.xticks(ticks_pixels, ticks_kbp)
plt.yticks(ticks_pixels, ticks_kbp)
plt.xlabel('relative position, kbp')
plt.ylabel('relative position, kbp')
plt.show()
This page was generated with nbsphinx from /home/docs/checkouts/readthedocs.org/user_builds/cooltools/checkouts/stable/docs/notebooks/pileup_CTCF.ipynb
Command line interface
Welcome to the cooltools command line interface (CLI) notebook!
Cooltools features a paired python API & CLI that enables user-facing functions to be run from the command line.
[1]:
import os, subprocess
import pandas as pd
import bioframe
import cooltools
import cooler
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
plt.rcParams['font.size']=12
from packaging import version
if version.parse(cooltools.__version__) < version.parse('0.5.2'):
raise AssertionError("tutorials rely on cooltools version 0.5.2 or higher,"+
"please check your cooltools version and update to the latest")
# We can use this function to display a file within the notebook
from IPython.display import Image
# download test data
# this file is 145 Mb, and may take a few seconds to download
cool_file = cooltools.download_data("HFF_MicroC", cache=True, data_dir='./data/')
print(cool_file)
# To use this variable in a bash call from jupyter just use $cool_file
./data/test.mcool
[2]:
%%bash
mkdir -p data
mkdir -p outputs
[3]:
# Note for the correct bash environment to be recognized from jupyter with the ! magic,
# jupyter notebook must be initialized from a conda environment with cooler and cooltools installed.
To see a list of CLI commands for cooltools, see the help:
[4]:
!cooltools -h
Usage: cooltools [OPTIONS] COMMAND [ARGS]...
Type -h or --help after any subcommand for more information.
Options:
-v, --verbose Verbose logging
-d, --debug Post mortem debugging
-V, --version Show the version and exit.
-h, --help Show this message and exit.
Commands:
coverage Calculate the sums of cis and genome-wide contacts (aka...
dots Call dots on a Hi-C heatmap that are not larger than...
eigs-cis Perform eigen value decomposition on a cooler matrix to...
eigs-trans Perform eigen value decomposition on a cooler matrix to...
expected-cis Calculate expected Hi-C signal for cis regions of...
expected-trans Calculate expected Hi-C signal for trans regions of...
genome Utilities for binned genome assemblies.
insulation Calculate the diamond insulation scores and call...
pileup Perform retrieval of the snippets from .cool file.
random-sample Pick a random sample of contacts from a Hi-C map.
saddle Calculate saddle statistics and generate saddle plots...
virtual4c Generate virtual 4C profile from a contact map by...
Visualization
[5]:
!cooler show $cool_file::resolutions/1000000 'chr2' -o 'outputs/chr2.png'
Traceback (most recent call last):
File "/Users/geofffudenberg/anaconda3/envs/open2c/bin/cooler", line 8, in <module>
sys.exit(cli())
File "/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/cooler/cli/show.py", line 230, in show
plt.gcf().canvas.set_window_title("Contact matrix".format())
AttributeError: 'FigureCanvasAgg' object has no attribute 'set_window_title'
[6]:
Image('outputs/chr2.png', width=400, height=400)
[6]:
Expected
Tables of expected counts, either in cis or trans, are key inputs for many downstream analyses in cooltools. For more details, see the contacts_vs_dist notebook.
Typically, we specify a view to define regions under analysis. Here we quickly create a view that specifies chromosome arms using tables of chromosome sizes and centromere positions.
[7]:
# create a view of hg38 chromosome arms using chromosome sizes and definition of centromeres
hg38_chromsizes = bioframe.fetch_chromsizes('hg38')
hg38_cens = bioframe.fetch_centromeres('hg38')
view_hg38 = bioframe.make_chromarms(hg38_chromsizes, hg38_cens)
# select only those chromosomes available in cooler
clr = cooler.Cooler(f'{cool_file}::/resolutions/1000000')
view_hg38 = view_hg38[view_hg38.chrom.isin(clr.chromnames)].reset_index(drop=True)
view_hg38.to_csv("data/view_hg38.tsv", index=False, header=False, sep='\t')
[8]:
! cooltools expected-cis $cool_file::resolutions/100000 --nproc 6 -o 'outputs/test.expected.cis.100000.tsv' --view "data/view_hg38.tsv"
Note expected for the first two distances are not defined with default settings, due to masking of near-diagonals in the cooler.
[9]:
display(
pd.read_table("outputs/test.expected.cis.100000.tsv")[0:5]
)
| region1 | region2 | dist | n_valid | count.sum | balanced.sum | count.avg | balanced.avg | |
|---|---|---|---|---|---|---|---|---|
| 0 | chr2_p | chr2_p | 0 | 878 | NaN | NaN | NaN | NaN |
| 1 | chr2_p | chr2_p | 1 | 876 | NaN | NaN | NaN | NaN |
| 2 | chr2_p | chr2_p | 2 | 874 | 2738583.0 | 65.287351 | 3133.390160 | 0.074699 |
| 3 | chr2_p | chr2_p | 3 | 872 | 1739972.0 | 41.011675 | 1995.380734 | 0.047032 |
| 4 | chr2_p | chr2_p | 4 | 870 | 1184707.0 | 28.473626 | 1361.732184 | 0.032728 |
Compartments & saddles
Many contact maps display plaid patterns of interactions. For more detail see the compartments notebook.
Since the orientation of eigenvectors is determined up to a sign, we often use GC content to orient or “phase” eigenvectors. Before calculating comparments, this notebook generates a binned GC content profile for the relevant region.
[10]:
## fasta sequence is required for calculating binned profile of GC conent
if not os.path.isfile('./data/hg38.fa'):
## note downloading a ~1Gb file can take a minute
subprocess.call('wget -P ./data --progress=bar:force:noscroll https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.fa.gz', shell=True)
subprocess.call('gunzip ./data/hg38.fa.gz', shell=True)
Bins can be fetched from the cooler, dropping any weights columns & keeping the header.
[11]:
!cooler dump --header -t bins $cool_file::resolutions/100000 | cut -f1-3 > outputs/bins.100000.tsv
[12]:
!cooltools genome gc outputs/bins.100000.tsv data/hg38.fa > outputs/gc.100000.tsv
[13]:
!cooltools eigs-cis -o outputs/test.eigs.100000 --view data/view_hg38.tsv --phasing-track outputs/gc.100000.tsv --n-eigs 1 $cool_file::resolutions/100000
/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/cooltools/lib/checks.py:550: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning.
for name, group in track.groupby([track.columns[0]]):
[14]:
display(
pd.read_table('outputs/test.eigs.100000.cis.vecs.tsv')[0:5]
)
| chrom | start | end | weight | E1 | |
|---|---|---|---|---|---|
| 0 | chr2 | 0 | 100000 | 0.006754 | -1.564658 |
| 1 | chr2 | 100000 | 200000 | 0.006767 | -1.747567 |
| 2 | chr2 | 200000 | 300000 | 0.004638 | -0.370827 |
| 3 | chr2 | 300000 | 400000 | 0.006034 | -1.326894 |
| 4 | chr2 | 400000 | 500000 | 0.006153 | -1.434981 |
Pairwise class averaging is a typical way to reveal preferences in contact frequencies between regions.
[15]:
!cooltools saddle --qrange 0.02 0.98 --fig png -o outputs/test.saddle.cis.100000 --view data/view_hg38.tsv $cool_file::resolutions/100000 outputs/test.eigs.100000.cis.vecs.tsv outputs/test.expected.cis.100000.tsv
/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/cooltools/lib/checks.py:550: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning.
for name, group in track.groupby([track.columns[0]]):
/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/cooltools/lib/checks.py:550: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning.
for name, group in track.groupby([track.columns[0]]):
/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/cooltools/lib/checks.py:550: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning.
for name, group in track.groupby([track.columns[0]]):
/Users/geofffudenberg/anaconda3/envs/open2c/lib/python3.9/site-packages/cooltools/lib/checks.py:550: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning.
for name, group in track.groupby([track.columns[0]]):
[16]:
saddle = np.load('outputs/test.saddle.cis.100000.saddledump.npz', allow_pickle=True)
[17]:
plt.figure(figsize=(6,6))
norm = LogNorm( vmin=10**(-1), vmax=10**1)
im = plt.imshow(
saddle['saddledata'],
cmap='RdBu_r',
norm = norm
);
plt.xlabel("saddle category")
plt.ylabel("saddle category")
plt.colorbar(im, label='obs/exp', pad=0.025, shrink=0.7);
Insulation & boundaries
A common strategy to summarize the near-diagonal structure of a contact map is by computing insulation scores. See the insulation notebook for more details.
The command below uses the Li method to threshold the insulation score for boundary calling, so the resulting table has both log2 insulation scores and whether a given region is a boundary. The boundary_strength_{window} column has a value for all local minima of the insulation profile, and the is_boundary_{window} column indicates whether this strength passed the threshold. Note that {window} indicates the chosen size of the sliding diamond, and the command below uses windows of size 100kb and 200kb.
[18]:
! cooltools insulation --threshold Li -o 'outputs/test.insulation.10000.tsv' --view "data/view_hg38.tsv" $cool_file::resolutions/10000 100000 200000
[19]:
display(
pd.read_table('outputs/test.insulation.10000.tsv')[0:5]
)
| chrom | start | end | region | is_bad_bin | log2_insulation_score_100000 | n_valid_pixels_100000 | log2_insulation_score_200000 | n_valid_pixels_200000 | boundary_strength_100000 | boundary_strength_200000 | is_boundary_100000 | is_boundary_200000 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr2 | 0 | 10000 | chr2_p | True | NaN | 0.0 | NaN | 0.0 | NaN | NaN | False | False |
| 1 | chr2 | 10000 | 20000 | chr2_p | False | 0.692051 | 8.0 | 1.123245 | 18.0 | NaN | NaN | False | False |
| 2 | chr2 | 20000 | 30000 | chr2_p | False | 0.760561 | 17.0 | 1.196643 | 37.0 | NaN | NaN | False | False |
| 3 | chr2 | 30000 | 40000 | chr2_p | False | 0.766698 | 27.0 | 1.211748 | 57.0 | NaN | NaN | False | False |
| 4 | chr2 | 40000 | 50000 | chr2_p | False | 0.674906 | 37.0 | 1.135037 | 77.0 | NaN | NaN | False | False |
Dots & focal enrichment
Punctate pairwise peaks of enriched contact frequency are a prevalent feature of mammalian interphase contact maps. See the dots notebook for more details.
Since dots are evident at higher resolutions, we first calculate the 10kb expected, and we used multiple cores to speed up the calculation.
[20]:
! cooltools expected-cis --nproc 6 -o 'outputs/test.expected.cis.10000.tsv' --view "data/view_hg38.tsv" $cool_file::resolutions/10000
[21]:
! cooltools dots --nproc 6 -o 'outputs/test.dots.10000.tsv' --view "data/view_hg38.tsv" $cool_file::resolutions/10000 outputs/test.expected.cis.10000.tsv
INFO:root:Using recommended donut-based kernels with w=5, p=2 for binsize=10000
INFO:root: matrix 9314X9314 to be split into 256 tiles of 600X600.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 14907X14907 to be split into 625 tiles of 600X600.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 2472X2472 to be split into 25 tiles of 600X600.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root: matrix 5855X5855 to be split into 100 tiles of 600X600.
INFO:root: tiles are padded (width=5) to enable convolution near the edges
INFO:root:convolving 108 tiles to build histograms for lambda-bins
INFO:root:creating a Pool of 6 workers to tackle 108 tiles
INFO:root:Done building histograms in 17.489 sec ...
INFO:root:Determined thresholds for every lambda-bin ...
INFO:root:convolving 108 tiles to extract enriched pixels
INFO:root:creating a Pool of 6 workers to tackle 108 tiles
INFO:root:Done extracting enriched pixels in 18.971 sec ...
INFO:root:Begin post-processing of 11284 filtered pixels
INFO:root:preparing to extract needed q-values ...
INFO:root:clustering enriched pixels in region: chr17_p
INFO:root:detected 198 clusters of 3.69+/-3.15 size
INFO:root:clustering enriched pixels in region: chr17_q
INFO:root:detected 584 clusters of 3.87+/-3.44 size
INFO:root:clustering enriched pixels in region: chr2_p
INFO:root:detected 841 clusters of 3.82+/-3.56 size
INFO:root:clustering enriched pixels in region: chr2_q
INFO:root:detected 1364 clusters of 3.72+/-3.24 size
INFO:root:Clustering is complete
INFO:root:filtered 2548 out of 2987 centroids to reduce the number of false-positives
[22]:
display(
pd.read_table('outputs/test.dots.10000.tsv')[0:5]
)
| chrom1 | start1 | end1 | chrom2 | start2 | end2 | count | la_exp.donut.value | la_exp.vertical.value | la_exp.horizontal.value | ... | la_exp.vertical.qval | la_exp.horizontal.qval | la_exp.lowleft.qval | region | cstart1 | cstart2 | c_label | c_size | region1 | region2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | chr17 | 12250000 | 12260000 | chr17 | 12740000 | 12750000 | 186 | 72.485199 | 79.603089 | 72.129599 | ... | 2.210430e-22 | 2.032096e-22 | 1.506741e-33 | chr17_p | 1.220571e+07 | 1.273857e+07 | 0 | 7 | chr17_p | chr17_p |
| 1 | chr17 | 10640000 | 10650000 | chr17 | 11980000 | 11990000 | 64 | 20.549081 | 23.891314 | 25.102296 | ... | 1.368050e-08 | 1.294897e-08 | 8.847705e-09 | chr17_p | 1.063000e+07 | 1.195500e+07 | 1 | 4 | chr17_p | chr17_p |
| 2 | chr17 | 9920000 | 9930000 | chr17 | 10610000 | 10620000 | 444 | 40.054241 | 75.104470 | 41.227788 | ... | 3.310219e-171 | 7.071107e-246 | 2.515747e-246 | chr17_p | 9.920000e+06 | 1.061200e+07 | 2 | 4 | chr17_p | chr17_p |
| 3 | chr17 | 10640000 | 10650000 | chr17 | 10840000 | 10850000 | 340 | 34.137182 | 46.658333 | 48.204555 | ... | 2.637572e-154 | 1.768044e-154 | 4.524004e-183 | chr17_p | 1.063667e+07 | 1.083889e+07 | 3 | 9 | chr17_p | chr17_p |
| 4 | chr17 | 12180000 | 12190000 | chr17 | 13000000 | 13010000 | 215 | 28.235042 | 36.990608 | 38.266379 | ... | 7.841810e-80 | 1.045765e-79 | 7.967002e-80 | chr17_p | 1.218571e+07 | 1.299143e+07 | 4 | 7 | chr17_p | chr17_p |
5 rows × 22 columns
Pileups & average features
A common method for quantifying contact maps is by creating pileup plots, which are averages over a set of “snippets”, or 2D windows, from the genome-wide map. See the pileups notebook for more details.
Below shows pileup for dots that were computed above.
[23]:
!cooltools pileup --features-format BEDPE --nproc 6 -o 'outputs/test.pileup.10000.npz' --view "data/view_hg38.tsv" --expected outputs/test.expected.cis.10000.tsv $cool_file::resolutions/10000 outputs/test.dots.10000.tsv
[24]:
## output is saved as an npz with keys 'pileup' and 'stack'
resolution = 10000
pile = np.load( f'outputs/test.pileup.{resolution}.npz')
[25]:
plt.figure(figsize=(6,6))
norm = LogNorm( vmin=10**(-1), vmax=10**1)
im = plt.imshow(
pile['pileup'],
cmap='RdBu_r',
norm = norm
);
plt.xticks(np.arange(0,25,5).astype(int),
(np.arange(0,25,5).astype(int)-10)*resolution//1000,
)
plt.yticks(np.arange(0,25,5).astype(int),
(np.arange(0,25,5).astype(int)-10)*resolution//1000,
)
plt.xlabel("offset from pileup center, kb")
plt.ylabel("offset from pileup center, kb")
plt.colorbar(im, label='obs/exp', pad=0.025, shrink=0.7);
This page was generated with nbsphinx from /home/docs/checkouts/readthedocs.org/user_builds/cooltools/checkouts/stable/docs/notebooks/command_line_interface.ipynb
Note that these notebooks currently focus on mammalian interphase Hi-C analysis, but are readily extendible to other organisms and cellular contexts. To clone and work interactively with these notebooks, visit: https://github.com/open2c/open2c_examples.
CLI Reference
cooltools
Type -h or –help after any subcommand for more information.
cooltools [OPTIONS] COMMAND [ARGS]...
Options
- -v, --verbose
Verbose logging
- -d, --debug
Post mortem debugging
- -V, --version
Show the version and exit.
coverage
Calculate the sums of cis and genome-wide contacts (aka coverage aka marginals) for a sparse Hi-C contact map in Cooler HDF5 format. Note that the sum(tot_cov) from this function is two times the number of reads contributing to the cooler, as each side contributes to the coverage.
COOL_PATH : The paths to a .cool file with a balanced Hi-C map.
cooltools coverage [OPTIONS] COOL_PATH
Options
- -o, --output <output>
Specify output file name to store the coverage in a tsv format.
- --ignore-diags <ignore_diags>
The number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.
- --store
Append columns with coverage (cov_cis_raw, cov_tot_raw), or (cov_cis_clr_weight_name, cov_tot_clr_weight_name) if calculating balanced coverage, to the cooler bin table. If clr_weight_name=None, also stores total cis counts in the cooler info
- --chunksize <chunksize>
Split the contact matrix pixel records into equally sized chunks to save memory and/or parallelize. Default is 10^7
- Default
10000000.0
- --bigwig
Also save output as bigWig files for cis and total coverage with the names <output>.<cis/tot>.bw
- --clr_weight_name <clr_weight_name>
Name of the weight column. Specify to calculate coverage of balanced cooler.
- -p, --nproc <nproc>
Number of processes to split the work between. [default: 1, i.e. no process pool]
Arguments
- COOL_PATH
Required argument
dots
Call dots on a Hi-C heatmap that are not larger than max_loci_separation.
COOL_PATH : The paths to a .cool file with a balanced Hi-C map.
EXPECTED_PATH : The paths to a tsv-like file with expected signal, including a header. Use the ‘::’ syntax to specify a column name.
Analysis will be performed for chromosomes referred to in EXPECTED_PATH, and therefore these chromosomes must be a subset of chromosomes referred to in COOL_PATH. Also chromosomes refered to in EXPECTED_PATH must be non-trivial, i.e., contain not-NaN signal. Thus, make sure to prune your EXPECTED_PATH before applying this script.
COOL_PATH and EXPECTED_PATH must be binned at the same resolution.
EXPECTED_PATH must contain at least the following columns for cis contacts: ‘region1/2’, ‘dist’, ‘n_valid’, value_name. value_name is controlled using options. Header must be present in a file.
cooltools dots [OPTIONS] COOL_PATH EXPECTED_PATH
Options
- --view, --regions <view>
Path to a BED file with the definition of viewframe (regions) used in the calculation of EXPECTED_PATH. Dot-calling will be performed for these regions independently e.g. chromosome arms. Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- --clr-weight-name <clr_weight_name>
Use cooler balancing weight with this name.
- Default
weight
- -p, --nproc <nproc>
Number of processes to split the work between. [default: 1, i.e. no process pool]
- --max-loci-separation <max_loci_separation>
Limit loci separation for dot-calling, i.e., do not call dots for loci that are further than max_loci_separation basepair apart. 2-20MB is reasonable and would capture most of CTCF-dots.
- Default
2000000
- --max-nans-tolerated <max_nans_tolerated>
Maximum number of NaNs tolerated in a footprint of every used filter. Must be controlled with caution, as large max-nans-tolerated, might lead to pixels scored in the padding area of the tiles to “penetrate” to the list of scored pixels for the statistical testing. [max-nans-tolerated <= 2*w ]
- Default
1
- --tile-size <tile_size>
Tile size for the Hi-C heatmap tiling. Typically on order of several mega-bases, and <= max_loci_separation.
- Default
6000000
- --num-lambda-bins <num_lambda_bins>
Number of log-spaced bins to divide your adjusted expected between. Same as HiCCUPS_W1_MAX_INDX (40) in the original HiCCUPS.
- Default
45
- --fdr <fdr>
False discovery rate (FDR) to control in the multiple hypothesis testing BH-FDR procedure.
- Default
0.02
- --clustering-radius <clustering_radius>
Radius for clustering dots that have been called too close to each other.Typically on order of 40 kilo-bases, and >= binsize.
- Default
39000
- -v, --verbose
Enable verbose output
- -o, --output <output>
Required Specify output file name to store called dots in a BEDPE-like format
Arguments
- COOL_PATH
Required argument
- EXPECTED_PATH
Required argument
eigs-cis
Perform eigen value decomposition on a cooler matrix to calculate compartment signal by finding the eigenvector that correlates best with the phasing track.
COOL_PATH : the paths to a .cool file with a balanced Hi-C map. Use the ‘::’ syntax to specify a group path in a multicooler file.
TRACK_PATH : the path to a BedGraph-like file that stores phasing track as track-name named column.
BedGraph-like format assumes tab-separated columns chrom, start, stop and track-name.
cooltools eigs-cis [OPTIONS] COOL_PATH
Options
- --phasing-track <TRACK_PATH>
Phasing track for orienting and ranking eigenvectors,provided as /path/to/track::track_value_column_name.
- --view, --regions <view>
Path to a BED file which defines which regions of the chromosomes to use (only implemented for cis contacts). Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- --n-eigs <n_eigs>
Number of eigenvectors to compute.
- Default
3
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name. Using raw unbalanced data is not currently supported for eigenvectors.
- Default
weight
- --ignore-diags <ignore_diags>
The number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.
- -v, --verbose
Enable verbose output
- -o, --out-prefix <out_prefix>
Required Save compartment track as a BED-like file. Eigenvectors and corresponding eigenvalues are stored in out_prefix.contact_type.vecs.tsv and out_prefix.contact_type.lam.txt
- --bigwig
Also save compartment track (E1) as a bigWig file with the name out_prefix.contact_type.bw
Arguments
- COOL_PATH
Required argument
eigs-trans
Perform eigen value decomposition on a cooler matrix to calculate compartment signal by finding the eigenvector that correlates best with the phasing track.
COOL_PATH : the paths to a .cool file with a balanced Hi-C map. Use the ‘::’ syntax to specify a group path in a multicooler file.
TRACK_PATH : the path to a BedGraph-like file that stores phasing track as track-name named column.
BedGraph-like format assumes tab-separated columns chrom, start, stop and track-name.
cooltools eigs-trans [OPTIONS] COOL_PATH
Options
- --phasing-track <TRACK_PATH>
Phasing track for orienting and ranking eigenvectors,provided as /path/to/track::track_value_column_name.
- --view, --regions <view>
Path to a BED file which defines which regions of the chromosomes to use (only implemented for cis contacts). Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- --n-eigs <n_eigs>
Number of eigenvectors to compute.
- Default
3
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name. Using raw unbalanced data is not supported for saddles.
- Default
weight
- -v, --verbose
Enable verbose output
- -o, --out-prefix <out_prefix>
Required Save compartment track as a BED-like file. Eigenvectors and corresponding eigenvalues are stored in out_prefix.contact_type.vecs.tsv and out_prefix.contact_type.lam.txt
- --bigwig
Also save compartment track (E1) as a bigWig file with the name out_prefix.contact_type.bw
Arguments
- COOL_PATH
Required argument
expected-cis
Calculate expected Hi-C signal for cis regions of chromosomal interaction map: average of interactions separated by the same genomic distance, i.e. are on the same diagonal on the cis-heatmap.
When balancing weights are not applied to the data, there is no masking of bad bins performed.
COOL_PATH : The paths to a .cool file with a balanced Hi-C map.
cooltools expected-cis [OPTIONS] COOL_PATH
Options
- -p, --nproc <nproc>
Number of processes to split the work between.[default: 1, i.e. no process pool]
- -c, --chunksize <chunksize>
Control the number of pixels handled by each worker process at a time.
- Default
10000000
- -o, --output <output>
Specify output file name to store the expected in a tsv format.
- --view, --regions <view>
Path to a 3 or 4-column BED file with genomic regions to calculated cis-expected on. When region names are not provided (no 4th column), UCSC-style region names are generated. Cis-expected is calculated for all chromosomes, when this is not specified. Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- --smooth
If set, cis-expected is smoothed and result stored in an additional column e.g. balanced.avg.smoothed
- --aggregate-smoothed
If set, cis-expected is averaged over all regions and then smoothed. Result is stored in an additional column, e.g. balanced.avg.smoothed.agg. Ignored without smoothing
- --smooth-sigma <smooth_sigma>
Control smoothing with the standard deviation of the smoothing Gaussian kernel, ignored without smoothing.
- Default
0.1
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name stored in cooler.Provide empty argument to calculate cis-expected on raw data
- Default
weight
- --ignore-diags <ignore_diags>
Number of diagonals to neglect for cis contact type
- Default
2
Arguments
- COOL_PATH
Required argument
expected-trans
Calculate expected Hi-C signal for trans regions of chromosomal interaction map: average of interactions in a rectangular block defined by a pair of regions, e.g. inter-chromosomal blocks.
When balancing weights are not applied to the data, there is no masking of bad bins performed.
COOL_PATH : The paths to a .cool file with a balanced Hi-C map.
cooltools expected-trans [OPTIONS] COOL_PATH
Options
- -p, --nproc <nproc>
Number of processes to split the work between.[default: 1, i.e. no process pool]
- -c, --chunksize <chunksize>
Control the number of pixels handled by each worker process at a time.
- Default
10000000
- -o, --output <output>
Specify output file name to store the expected in a tsv format.
- --view, --regions <view>
Path to a 3 or 4-column BED file with genomic regions. Trans-expected is calculated on all pairwise combinations of these regions. When region names are not provided (no 4th column), UCSC-style region names are generated. Trans-expected is calculated for all inter-chromosomal pairs, when view is not specified. Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name stored in cooler.Provide empty argument to calculate cis-expected on raw data
- Default
weight
Arguments
- COOL_PATH
Required argument
genome
Utilities for binned genome assemblies.
cooltools genome [OPTIONS] COMMAND [ARGS]...
cooltools genome binnify [OPTIONS] CHROMSIZES_PATH BINSIZE
Options
- --all-names
Parse all chromosome names from file, not only default r”^chr[0-9]+$”, r”^chr[XY]$”, r”^chrM$”.
Arguments
- CHROMSIZES_PATH
Required argument
- BINSIZE
Required argument
cooltools genome digest [OPTIONS] CHROMSIZES_PATH FASTA_PATH ENZYME_NAME
Arguments
- CHROMSIZES_PATH
Required argument
- FASTA_PATH
Required argument
- ENZYME_NAME
Required argument
insulation
Calculate the diamond insulation scores and call insulating boundaries.
IN_PATH : The path to a .cool file with a balanced Hi-C map.
- WINDOWThe window size for the insulation score calculations.
Multiple space-separated values can be provided. By default, the window size must be provided in units of bp. When the flag –window-pixels is set, the window sizes must be provided in units of pixels instead.
cooltools insulation [OPTIONS] IN_PATH WINDOW
Options
- -p, --nproc <nproc>
Number of processes to split the work between.[default: 1, i.e. no process pool]
- -o, --output <output>
Specify output file name to store the insulation in a tsv format.
- --view, --regions <view>
Path to a BED file containing genomic regions for which insulation scores will be calculated. Region names can be provided in a 4th column and should match regions and their names in expected. Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- --ignore-diags <ignore_diags>
The number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name. Provide empty argument to calculate insulation on raw data (no masking bad pixels).
- Default
weight
- --min-frac-valid-pixels <min_frac_valid_pixels>
The minimal fraction of valid pixels in a sliding diamond. Used to mask bins during boundary detection.
- Default
0.66
- --min-dist-bad-bin <min_dist_bad_bin>
The minimal allowed distance to a bad bin. Use to mask bins after insulation calculation and during boundary detection.
- Default
0
- --threshold <threshold>
Rule used to threshold the histogram of boundary strengths to exclude weakboundaries. ‘Li’ or ‘Otsu’ use corresponding methods from skimage.thresholding.Providing a float value will filter by a fixed threshold
- Default
0
- --window-pixels
If set then the window sizes are provided in units of pixels.
- --append-raw-scores
Append columns with raw scores (sum_counts, sum_balanced, n_pixels) to the output table.
- --chunksize <chunksize>
- Default
20000000
- --verbose
Report real-time progress.
- --bigwig
Also save insulation tracks as a bigWig files for different window sizes with the names output.<window-size>.bw
Arguments
- IN_PATH
Required argument
- WINDOW
Optional argument(s)
pileup
Perform retrieval of the snippets from .cool file.
COOL_PATH : The paths to a .cool file with a balanced Hi-C map. Use the ‘::’ syntax to specify a group path in a multicooler file.
FEATURES_PATH : the path to a BED or BEDPE-like file that contains features for snipping windows. If BED, then the features are on-diagonal. If BEDPE, then the features can be off-diagonal (but not in trans or between different regions in the view).
cooltools pileup [OPTIONS] COOL_PATH FEATURES_PATH
Options
- --view, --regions <view>
Path to a BED file which defines which regions of the chromosomes to use. Required if EXPECTED_PATH is provided Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- --expected <expected>
Path to the expected table. If provided, outputs OOE pileup. if not provided, outputs regular pileup.
- --flank <flank>
Size of flanks.
- Default
100000
- --features-format <features_format>
Input features format.
- Options
auto | BED | BEDPE
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name.
- Default
weight
- -o, --out <out>
Required Save output pileup as NPZ/HDF5 file.
- --out-format <out_format>
Type of output.
- Default
NPZ- Options
NPZ | HDF5
- --store-snips
Flag indicating whether snips should be stored.
- -p, --nproc <nproc>
Number of processes to split the work between. [default: 1, i.e. no process pool]
- --ignore-diags <ignore_diags>
The number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.
- --aggregate <aggregate>
Function for calculating aggregate signal.
- Default
none- Options
none | mean | median | std | min | max
- -v, --verbose
Enable verbose output
Arguments
- COOL_PATH
Required argument
- FEATURES_PATH
Required argument
random-sample
Pick a random sample of contacts from a Hi-C map.
IN_PATH : Input cooler path or URI.
OUT_PATH : Output cooler path or URI.
Specify the target sample size with either –count or –frac.
cooltools random-sample [OPTIONS] IN_PATH OUT_PATH
Options
- -c, --count <count>
The target number of contacts in the sample. The resulting sample size will not match it precisely. Mutually exclusive with –frac and –cis-count
- --cis-count <cis_count>
The target number of cis contacts in the sample. The resulting sample size will not match it precisely. Mutually exclusive with –count and –frac
- -f, --frac <frac>
The target sample size as a fraction of contacts in the original dataset. Mutually exclusive with –count and –cis-count
- --exact
If specified, use exact sampling that guarantees the size of the output sample. Otherwise, binomial sampling will be used and the sample size will be distributed around the target value.
- -p, --nproc <nproc>
Number of processes to split the work between.[default: 1, i.e. no process pool]
- --chunksize <chunksize>
The number of pixels loaded and processed per step of computation.
- Default
10000000
Arguments
- IN_PATH
Required argument
- OUT_PATH
Required argument
rearrange
Rearrange data from a cooler according to a new genomic view
- IN_PATHstr
.cool file (or URI) with data to rearrange.
- OUT_PATHstr
.cool file (or URI) to save the rearrange data.
- viewstr
Path to a BED-like file which defines which regions of the chromosomes to use and in what order. Has to be a valid viewframe (columns corresponding to region coordinates followed by the region name), with potential additional columns. Using –new-chrom-col and –orientation-col you can specify the new chromosome names and whether to invert each region (optional). If has no header with column names, assumes the new-chrom-col is the fifth column and –orientation-col is the sixth, if they exist.
- new_chrom_colstr
Column name in the view with new chromosome names. If not provided and there is no column named ‘new_chrom’ in the view file, uses original chromosome names.
- orientation_colstr
Columns name in the view with orientations of each region (+ or -). - means the region will be inverted. If not providedand there is no column named ‘strand’ in the view file, assumes all are forward oriented.
- assemblystr
The name of the assembly for the new cooler. If None, uses the same as in the original cooler.
- chunksizeint
The number of pixels loaded and processed per step of computation.
- modestr
(w)rite or (a)ppend to the output file (default: w)
cooltools rearrange [OPTIONS] IN_PATH OUT_PATH
Options
- --view <view>
Required Path to a BED-like file which defines which regions of the chromosomes to use and in what order. Using –new-chrom-col and –orientation-col you can specify the new chromosome names and whether to invert each region (optional)
- --new-chrom-col <new_chrom_col>
Column name in the view with new chromosome names. If not provided and there is no column named ‘new_chrom’ in the view file, uses original chromosome names
- --orientation-col <orientation_col>
Columns name in the view with orientations of each region (+ or -). If not providedand there is no column named ‘strand’ in the view file, assumes all are forward oriented
- --assembly <assembly>
The name of the assembly for the new cooler. If None, uses the same as in the original cooler.
- --chunksize <chunksize>
The number of pixels loaded and processed per step of computation.
- Default
10000000
- --mode <mode>
(w)rite or (a)ppend to the output file (default: w)
- Options
w | a
Arguments
- IN_PATH
Required argument
- OUT_PATH
Required argument
saddle
Calculate saddle statistics and generate saddle plots for an arbitrary signal track on the genomic bins of a contact matrix.
COOL_PATH : The paths to a .cool file with a balanced Hi-C map. Use the ‘::’ syntax to specify a group path in a multicooler file.
TRACK_PATH : The path to bedGraph-like file with a binned compartment track (eigenvector), including a header. Use the ‘::’ syntax to specify a column name.
EXPECTED_PATH : The paths to a tsv-like file with expected signal, including a header. Use the ‘::’ syntax to specify a column name.
Analysis will be performed for chromosomes referred to in TRACK_PATH, and therefore these chromosomes must be a subset of chromosomes referred to in COOL_PATH and EXPECTED_PATH.
COOL_PATH, TRACK_PATH and EXPECTED_PATH must be binned at the same resolution (expect for EXPECTED_PATH in case of trans contact type).
EXPECTED_PATH must contain at least the following columns for cis contacts: ‘chrom’, ‘diag’, ‘n_valid’, value_name and the following columns for trans contacts: ‘chrom1’, ‘chrom2’, ‘n_valid’, value_name value_name is controlled using options. Header must be present in a file.
cooltools saddle [OPTIONS] COOL_PATH TRACK_PATH EXPECTED_PATH
Options
- -t, --contact-type <contact_type>
Type of the contacts to aggregate
- Default
cis- Options
cis | trans
- --min-dist <min_dist>
Minimal distance between bins to consider, bp. If negative, removesthe first two diagonals of the data. Ignored with –contact-type trans.
- Default
-1
- --max-dist <max_dist>
Maximal distance between bins to consider, bp. Ignored, if negative. Ignored with –contact-type trans.
- Default
-1
- -n, --n-bins <n_bins>
Number of bins for digitizing track values.
- Default
50
- --vrange <vrange>
Low and high values used for binning genome-wide track values, e.g. if range`=(-0.05, 0.05), `n-bins equidistant bins would be generated. Use to prevent extreme track values from exploding the bin range and to ensure consistent bins across several runs of compute_saddle command using different track files.
- --qrange <qrange>
Low and high values used for quantile bins of genome-wide track values,e.g. if `qrange`=(0.02, 0.98) the lower bin would start at the 2nd percentile and the upper bin would end at the 98th percentile of the genome-wide signal. Use to prevent the extreme track values from exploding the bin range.
- Default
None, None
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name.
- Default
weight
- --strength, --no-strength
Compute and save compartment ‘saddle strength’ profile
- --view, --regions <view>
Path to a BED file containing genomic regions for which saddleplot will be calculated. Region names can be provided in a 4th column and should match regions and their names in expected. Note that ‘–regions’ is the deprecated name of the option. Use ‘–view’ instead.
- -o, --out-prefix <out_prefix>
Required Dump ‘saddledata’, ‘binedges’ and ‘hist’ arrays in a numpy-specific .npz container. Use numpy.load to load these arrays into a dict-like object. The digitized signal values are saved to a bedGraph-style TSV.
- --fig <fig>
Generate a figure and save to a file of the specified format. If not specified - no image is generated. Repeat for multiple output formats.
- Options
png | jpg | svg | pdf | ps | eps
- --scale <scale>
Value scale for the heatmap
- Default
log- Options
linear | log
- --cmap <cmap>
Name of matplotlib colormap
- Default
coolwarm
- --vmin <vmin>
Low value of the saddleplot colorbar. Note: value in original units irrespective of used scale, and therefore should be positive for both vmin and vmax.
- --vmax <vmax>
High value of the saddleplot colorbar
- --hist-color <hist_color>
Face color of histogram bar chart
- -v, --verbose
Enable verbose output
Arguments
- COOL_PATH
Required argument
- TRACK_PATH
Required argument
- EXPECTED_PATH
Required argument
virtual4c
Generate virtual 4C profile from a contact map by extracting all interactions of a given viewpoint with the rest of the genome.
COOL_PATH : the paths to a .cool file with a Hi-C map. Use the ‘::’ syntax to specify a group path in a multicooler file.
VIEWPOINT : the viewpoint to use for the virtual 4C profile. Provide as a UCSC-string (e.g. chr1:1-1000)
Note: this is a new (experimental) tool, the interface or output might change in a future version.
cooltools virtual4c [OPTIONS] COOL_PATH VIEWPOINT
Options
- --clr-weight-name <clr_weight_name>
Use balancing weight with this name. Provide empty argument to calculate insulation on raw data (no masking bad pixels).
- Default
weight
- -o, --out-prefix <out_prefix>
Required Save virtual 4C track as a BED-like file. Contact frequency is stored in out_prefix.v4C.tsv
- --bigwig
Also save virtual 4C track as a bigWig file with the name out_prefix.v4C.bw
- -p, --nproc <nproc>
Number of processes to split the work between. [default: 1, i.e. no process pool]
Arguments
- COOL_PATH
Required argument
- VIEWPOINT
Required argument
API Reference
subpackages
cooltools.lib package
- cooltools.lib.common.align_track_with_cooler(track, clr, view_df=None, clr_weight_name='weight', mask_clr_bad_bins=True, drop_track_na=True)[source]
Sync a track dataframe with a cooler bintable.
Checks that bin sizes match between a track and a cooler, merges the cooler bintable with the track, and propagates masked regions from a cooler bintable to a track.
- Parameters
track (pd.DataFrame) – bedGraph-like track DataFrame to check
clr (cooler) – cooler object to check against
view_df (bioframe.viewframe or None) – Optional viewframe of regions to check for their number of bins with assigned track values. If None, constructs a view_df from cooler chromsizes.
clr_weight_name (str) – Name of the column in the bin table with weight
mask_clr_bad_bins (bool) – Whether to propagate null bins from cooler bintable column clr_weight_name to the ‘value’ column of the output clr_track. Default True.
drop_track_na (bool) – Whether to ignore missing values in the track (as if they are absent). Important for raising errors for unassigned regions and warnings for partial assignment. Default True, so NaN values are treated as not assigned. False means that NaN values are treated as assigned.
- Returns
clr_track – track dataframe that has been aligned with the cooler bintable and has columns [‘chrom’,’start’,’end’,’value’]
- cooltools.lib.common.assign_regions(features, supports)[source]
DEPRECATED. Will be removed in the future versions and replaced with bioframe.overlap() For each feature in features dataframe assign the genomic region (support) that overlaps with it. In case if feature overlaps multiple supports, the region with largest overlap will be reported.
- cooltools.lib.common.assign_supports(features, supports, labels=False, suffix='')[source]
Assign support regions to a table of genomic intervals. Obsolete, replaced by assign_regions now.
- Parameters
features (DataFrame) – Dataframe with columns chrom, start, end or chrom1, start1, end1, chrom2, start2, end2
supports (array-like) – Support areas
- cooltools.lib.common.assign_view_auto(features, view_df, cols_unpaired=['chrom', 'start', 'end'], cols_paired=['chrom1', 'start1', 'end1', 'chrom2', 'start2', 'end2'], cols_view=['chrom', 'start', 'end'], features_view_col_unpaired='region', features_view_cols_paired=['region1', 'region2'], view_name_col='name', drop_unassigned=False, combined_assignments_column='region', force=True)[source]
Assign region names from the view to each feature
Determines whether the features are unpaired (1D, bed-like) or paired (2D, bedpe-like) based on presence of column names (cols_unpaired vs cols_paired) Assigns a regular 1D view, independently to each side in case of paired features. Will add one or two columns with region names (features_view_col_unpaired or features_view_cols_paired) respectively, in case of unpaired and paired features.
- Parameters
features (pd.DataFrame) – bedpe-style dataframe
view_df (pandas.DataFrame) – ViewFrame specifying region start and ends for assignment. Attempts to convert dictionary and pd.Series formats to viewFrames.
cols_unpaired (list of str) – The names of columns containing the chromosome, start and end of the genomic intervals for unpaired features. The default values are “chrom”, “start”, “end”.
cols_paired (list of str) – The names of columns containing the chromosome, start and end of the genomic intervals for paired features. The default values are “chrom1”, “start1”, “end1”, “chrom2”, “start2”, “end2”.
cols_view (list of str) – The names of columns containing the chromosome, start and end of the genomic intervals in the view. The default values are “chrom”, “start”, “end”.
features_view_col_unpaired (str) – Name of the column where to save the assigned region name for unpaired features
features_view_cols_paired (list of str) – Names of the columns where to save the assigned region names for paired features
view_name_col (str) – Column of
view_dfwith region names. Default “name”.drop_unassigned (bool) – If True, drop intervals in features that do not overlap a region in the view. Default False.
combined_assignments_column (str or None) – If set to a string value, will combine assignments from two sides of paired features when they match into column with this name: region name when regions assigned to both sides match, np.nan if not. Default “region”
force (bool, True or False) – if features already have features_view_col (paired or not, depending on the feature types), should we re-wrtie region columns or keep them.
- cooltools.lib.common.assign_view_paired(features, view_df, cols_paired=['chrom1', 'start1', 'end1', 'chrom2', 'start2', 'end2'], cols_view=['chrom', 'start', 'end'], features_view_cols=['region1', 'region2'], view_name_col='name', drop_unassigned=False)[source]
Assign region names from the view to each feature
Assigns a regular 1D view independently to each side of a bedpe-style dataframe. Will add two columns with region names (features_view_cols)
- Parameters
features (pd.DataFrame) – bedpe-style dataframe
view_df (pandas.DataFrame) – ViewFrame specifying region start and ends for assignment. Attempts to convert dictionary and pd.Series formats to viewFrames.
cols_paired (list of str) – The names of columns containing the chromosome, start and end of the genomic intervals. The default values are “chrom1”, “start1”, “end1”, “chrom2”, “start2”, “end2”.
cols_view (list of str) – The names of columns containing the chromosome, start and end of the genomic intervals in the view. The default values are “chrom”, “start”, “end”.
features_view_cols (list of str) – Names of the columns where to save the assigned region names
view_name_col (str) – Column of
view_dfwith region names. Default “name”.drop_unassigned (bool) – If True, drop intervals in df that do not overlap a region in the view. Default False.
- cooltools.lib.common.make_cooler_view(clr, ucsc_names=False)[source]
Generate a full chromosome viewframe using cooler’s chromsizes
- Parameters
clr (cooler) – cooler-object to extract chromsizes
ucsc_names (bool) – Use full UCSC formatted names instead of short chromosome names.
- Returns
cooler_view (viewframe) – full chromosome viewframe
- cooltools.lib.common.mask_cooler_bad_bins(track, bintable)[source]
Mask (set to NaN) values in track where bin is masked in bintable.
Currently used in cli.get_saddle(). TODO: determine if this should be used elsewhere.
- Parameters
track (tuple of (DataFrame, str)) – bedGraph-like dataframe along with the name of the value column.
bintable (tuple of (DataFrame, str)) – bedGraph-like dataframe along with the name of the weight column.
- Returns
track (DataFrame) – New bedGraph-like dataframe with bad bins masked in the value column
- cooltools.lib.common.pool_decorator(func)[source]
A decorator function that enables multiprocessing for a given function. The function must have a
map_functorkeyword argument. It works by hijacking map_functor argument and substituting it with the parallel one: multiprocess.Pool(nproc).imap, when nproc > 1- Parameters
func (callable) – The function to be decorated.
- Returns
A wrapper function that enables multiprocessing for the given function.
- cooltools.lib.numutils.COMED(xs, ys, has_nans=False)[source]
Calculate the comedian - the robust median-based counterpart of Pearson’s r.
comedian = median((xs-median(xs))*(ys-median(ys))) / MAD(xs) / MAD(ys)
- Parameters
has_nans (bool) – if True, mask (x,y) pairs with at least one NaN
Notes
Citations: “On MAD and comedians” by Michael Falk (1997), “Robust Estimation of the Correlation Coefficient: An Attempt of Survey” by Georgy Shevlyakov and Pavel Smirnov (2011)
- cooltools.lib.numutils.MAD(arr, axis=None, has_nans=False)[source]
Calculate the Median Absolute Deviation from the median.
- Parameters
arr (np.ndarray) – Input data.
axis (int) – The axis along which to calculate MAD.
has_nans (bool) – If True, use the slower NaN-aware method to calculate medians.
- cooltools.lib.numutils.adaptive_coarsegrain(ar, countar, cutoff=5, max_levels=8, min_shape=8)[source]
Adaptively coarsegrain a Hi-C matrix based on local neighborhood pooling of counts.
- Parameters
ar (array_like, shape (n, n)) – A square Hi-C matrix to coarsegrain. Usually this would be a balanced matrix.
countar (array_like, shape (n, n)) – The raw count matrix for the same area. Has to be the same shape as the Hi-C matrix.
cutoff (float, optional) – A minimum number of raw counts per pixel required to stop 2x2 pooling. Larger cutoff values would lead to a more coarse-grained, but smoother map. 3 is a good default value for display purposes, could be lowered to 1 or 2 to make the map less pixelated. Setting it to 1 will only ensure there are no zeros in the map.
max_levels (int, optional) – How many levels of coarsening to perform. It is safe to keep this number large as very coarsened map will have large counts and no substitutions would be made at coarser levels.
min_shape (int, optional) – Stop coarsegraining when coarsegrained array shape is less than that.
- Returns
Smoothed array, shape (n, n)
Notes
The algorithm works as follows:
First, it pads an array with NaNs to the nearest power of two. Second, it coarsens the array in powers of two until the size is less than minshape.
Third, it starts with the most coarsened array, and goes one level up. It looks at all 4 pixels that make each pixel in the second-to-last coarsened array. If the raw counts for any valid (non-NaN) pixel are less than
cutoff, it replaces the values of the valid (4 or less) pixels with the NaN-aware average. It is then applied to the next (less coarsened) level until it reaches the original resolution.In the resulting matrix, there are guaranteed to be no zeros, unless very large zero-only areas were provided such that zeros were produced
max_levelstimes when coarsening.Examples
>>> c = cooler.Cooler("/path/to/some/cooler/at/about/2000bp/resolution")
>>> # sample region of about 6000x6000 >>> mat = c.matrix(balance=True).fetch("chr1:10000000-22000000") >>> mat_raw = c.matrix(balance=False).fetch("chr1:10000000-22000000") >>> mat_cg = adaptive_coarsegrain(mat, mat_raw)
>>> plt.figure(figsize=(16,7)) >>> ax = plt.subplot(121) >>> plt.imshow(np.log(mat), vmax=-3) >>> plt.colorbar() >>> plt.subplot(122, sharex=ax, sharey=ax) >>> plt.imshow(np.log(mat_cg), vmax=-3) >>> plt.colorbar()
- cooltools.lib.numutils.coarsen(reduction, x, axes, trim_excess=False)[source]
Coarsen an array by applying reduction to fixed size neighborhoods. Adapted from dask.array.coarsen to work on regular numpy arrays.
- Parameters
reduction (function) – Function like np.sum, np.mean, etc…
x (np.ndarray) – Array to be coarsened
axes (dict) – Mapping of axis to coarsening factor
trim_excess (bool, optional) – Remove excess elements. Default is False.
Examples
Provide dictionary of scale per dimension
>>> x = np.array([1, 2, 3, 4, 5, 6]) >>> coarsen(np.sum, x, {0: 2}) array([ 3, 7, 11])
>>> coarsen(np.max, x, {0: 3}) array([3, 6])
>>> x = np.arange(24).reshape((4, 6)) >>> x array([[ 0, 1, 2, 3, 4, 5], [ 6, 7, 8, 9, 10, 11], [12, 13, 14, 15, 16, 17], [18, 19, 20, 21, 22, 23]])
>>> coarsen(np.min, x, {0: 2, 1: 3}) array([[ 0, 3], [12, 15]])
See also
dask.array.coarsen
- cooltools.lib.numutils.dist_to_mask(mask, side='min')[source]
Calculate the distance to the nearest True element of an array.
- Parameters
mask (iterable of bool) – A boolean array.
side (str) – The side . Accepted values are: ‘left’ : calculate the distance to the nearest True value on the left ‘right’ : calculate the distance to the nearest True value on the right ‘min’ : calculate the distance to the closest True value ‘max’ : calculate the distance to the furthest of the two neighbouring True values
- Returns
dist (array of int)
Notes
The solution is borrowed from https://stackoverflow.com/questions/18196811/cumsum-reset-at-nan
- cooltools.lib.numutils.fill_diag(arr, x, i=0, copy=True)[source]
Identical to set_diag, but returns a copy by default
- cooltools.lib.numutils.fill_inf(arr, pos_value=0, neg_value=0, copy=True)[source]
Replaces positive and negative infinity entries in an array with the provided values.
- Parameters
arr (np.array) –
pos_value (float) – Fill value for np.inf
neg_value (float) – Fill value for -np.inf
copy (bool, optional) – If True, creates a copy of x, otherwise replaces values in-place. By default, True.
- cooltools.lib.numutils.fill_na(arr, value=0, copy=True)[source]
Replaces np.nan entries in an array with the provided value.
- Parameters
arr (np.array) –
value (float) –
copy (bool, optional) – If True, creates a copy of x, otherwise replaces values in-place. By default, True.
- cooltools.lib.numutils.fill_nainf(arr, value=0, copy=True)[source]
Replaces np.nan and np.inf entries in an array with the provided value.
- Parameters
arr (np.array) –
value (float) –
copy (bool, optional) – If True, creates a copy of x, otherwise replaces values in-place. By default, True.
Notes
Differs from np.nan_to_num in that it replaces np.inf with the same number as np.nan.
- cooltools.lib.numutils.get_diag(arr, i=0)[source]
Get the i-th diagonal of a matrix. This solution was borrowed from http://stackoverflow.com/questions/9958577/changing-the-values-of-the-diagonal-of-a-matrix-in-numpy
- cooltools.lib.numutils.get_eig(mat, n=3, mask_zero_rows=False, subtract_mean=False, divide_by_mean=False)[source]
Perform an eigenvector decomposition.
- Parameters
mat (np.ndarray) – A square matrix, must not contain nans, infs or zero rows.
n (int) – The number of eigenvectors to return. Output is backfilled with NaNs when n exceeds the size of the input matrix.
mask_zero_rows (bool) – If True, mask empty rows/columns before eigenvector decomposition. Works only with symmetric matrices.
subtract_mean (bool) – If True, subtract the mean from the matrix.
divide_by_mean (bool) – If True, divide the matrix by its mean.
- Returns
eigvecs (np.ndarray) – An array of eigenvectors (in rows), sorted by a decreasing absolute eigenvalue.
eigvals (np.ndarray) – An array of sorted eigenvalues.
- cooltools.lib.numutils.get_kernel(w, p, ktype)[source]
Return typical kernels given size parameteres w, p,and kernel type.
- Parameters
w (int) – Outer kernel size (actually half of it).
p (int) – Inner kernel size (half of it).
ktype (str) – Name of the kernel type, could be one of the following: ‘donut’, ‘vertical’, ‘horizontal’, ‘lowleft’, ‘upright’.
- Returns
kernel (ndarray) – A square matrix of int type filled with 1 and 0, according to the kernel type.
- cooltools.lib.numutils.interp_nan(a_init, pad_zeros=True, method='linear', verbose=False)[source]
Linearly interpolate to fill NaN rows and columns in a matrix. Also interpolates NaNs in 1D arrays.
- Parameters
a_init (np.array) –
pad_zeros (bool, optional) – If True, pads the matrix with zeros to fill NaNs at the edges. By default, True.
method (str, optional) – For 2D: “linear”, “nearest”, or “splinef2d” For 1D: “linear”, “nearest”, “zero”, “slinear”, “quadratic”, “cubic”
- Returns
array with NaNs linearly interpolated
Notes
1D case adapted from: https://stackoverflow.com/a/39592604 2D case assumes that entire rows or columns are masked & edges to be NaN-free, but is much faster than griddata implementation.
- cooltools.lib.numutils.interpolate_bad_singletons(mat, mask=None, fillDiagonal=True, returnMask=False, secondPass=True, verbose=False)[source]
Interpolate singleton missing bins for visualization
Examples
>>> ax = plt.subplot(121) >>> maxval = np.log(np.nanmean(np.diag(mat,3))*2 ) >>> plt.matshow(np.log(mat)), vmax=maxval, fignum=False) >>> plt.set_cmap('fall'); >>> plt.subplot(122, sharex=ax, sharey=ax) >>> plt.matshow( ... np.log(interpolate_bad_singletons(remove_good_singletons(mat))), ... vmax=maxval, ... fignum=False ... ) >>> plt.set_cmap('fall'); >>> plt.show()
- cooltools.lib.numutils.normalize_score(arr, norm='z', axis=None, has_nans=True)[source]
Normalize an array by subtracting the first moment and dividing the residual by the second.
- Parameters
arr (np.ndarray) – Input data.
norm (str) –
The type of normalization. ‘z’ - report z-scores, norm_arr = (arr - mean(arr)) / std(arr)
’mad’ - report deviations from the median in units of MAD (Median Absolute Deviation from the median), norm_arr = (arr - median(arr)) / MAD(arr)
’madz’ - report robust z-scores, i.e. estimate the mean as the median and the standard error as MAD / 0.67499, norm_arr = (arr - median(arr)) / MAD(arr) * 0.67499
axis (int) – The axis along which to calculate the normalization parameters.
has_nans (bool) – If True, use slower NaN-aware methods to calculate the normalization parameters.
- cooltools.lib.numutils.persistent_log_bins(end=10, bins_per_order_magnitude=10)[source]
Creates most nicely looking log-spaced integer bins starting at 1, with the defined number of bins per order of magnitude.
- Parameters
end (number (int recommended) log10 of the last value. It is safe to put a) –
later. (large value here and select your range of bins) –
bins_per_order_magnitude (int >0 how many bins per order of magnitude) –
Notes
This is not a replacement for logbins, and it has a different purpose.
Difference between this and logbins Logbins creates bins from lo to hi, spaced logarithmically with an appriximate ratio. Logbins makes sure that the last bin is large (i.e. hi/ratio … hi), and will not allow the last bin to be much less than ratio. It would slightly adjust the ratio to achieve that. As a result, by construciton, logbins bins are different for different lo or hi.
This function is designed to create exactly the same bins that only depend on one parameter, bins_per_order_magnitude. The goal is to make things calculated for different datasets/organisms/etc. comparable. For example, if these bins are used, it would allow us to divide P(s) for two different organisms by each other because it was calculated for the same bins.
The price you pay for such versatility is that the last bin can be much less than others in real application. For example, if you have 10 bins per order of magnitude (ratio of 1.25), but your data ends at 10500, then the only points in the last bin would be 10000..10500, 1/5 of what could be. This may make the last point noisy.
The main part is done using np.logspace and rounding to the nearest integer, followed by unique. The gaps are then re-sorted to ensure that gaps are strictly increasing. The re-sorting of gaps was essential, and produced better results than manual adjustment.
Alternatives that produce irregular bins Using np.unique(np.logspace(a,b,N,dtype=int)) can be sub-optimal For example, np.unique(np.logspace(0,1,11,dtype=int)) = [ 1, 2, 3, 5, 6, 7, 10] Note the gaps jump from 1 to 2 back to 1
Similarly using np.unique(np.rint(np.logspace..)) can be suboptimal np.unique(np.array(np.rint(np.logspace(0,1,9)),dtype=int)) = [ 1, 2, 3, 4, 6, 7, 10]
for bins_per_order_of_magnitude=16, 10 is not in bins. Other than that, 10, 100, 1000, etc. are always included.
- cooltools.lib.numutils.robust_gauss_filter(ar, sigma=2, functon=<Mock name='mock.gaussian_filter1d' id='139638368253312'>, kwargs=None)[source]
Implements an edge-handling mode for gaussian filter that basically ignores the edge, and also handles NaNs.
- Parameters
ar (array-like) – Input array
sigma (float) – sigma to be passed to the filter
function (callable) – Filter to use. Default is gauusian_filter1d
kwargs (dict) – Additional args to pass to the filter. Default:None
Notes
Available edge-handling modes in ndimage.filters attempt to somehow “extrapolate” the edge value and then apply the filter (see https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.convolve.html).
That’s likely because convolve uses fast fourier transform, which requires
the kernel to be constant. Here we design a better edge-handling for the gaussian smoothing.
In a gaussian-filtered array, a pixel away from the edge is a mean of nearby pixels with gaussian weights. With this mode, pixels near start/end are also a mean of nearby pixels with gaussian weights. That’s it. If we encounter NANs, we also simply ignore them, following the same definition: mean of nearby valid pixels. Yes, it raises the weights for the first/last pixels, because now only a part of the whole gaussian is being used (up to 1/2 for the first/last pixel and large sigma). But it preserves the “mean of nearby pixels” definition. It is different from padding with zeros (it would drag the first pixel down to be more like zero). It is also different from “nearest” - that gives too much weight to the first/last pixel.
To achieve this smoothing, we preform regular gaussian smoothing using mode=”constant” (pad with zeros). Then we take an array of valid pixels and smooth it the same way. This calculates how many “average valid pixels” contributed to each point of a smoothed array. Dividing one by the other achieves the desired result.
- cooltools.lib.numutils.set_diag(arr, x, i=0, copy=False)[source]
Rewrite the i-th diagonal of a matrix with a value or an array of values. Supports 2D arrays, square or rectangular. In-place by default.
- Parameters
arr (2-D array) – Array whose diagonal is to be filled.
x (scalar or 1-D vector of correct length) – Values to be written on the diagonal.
i (int, optional) – Which diagonal to write to. Default is 0. Main diagonal is 0; upper diagonals are positive and lower diagonals are negative.
copy (bool, optional) – Return a copy. Diagonal is written in-place if false. Default is False.
- Returns
Array with diagonal filled.
Notes
Similar to numpy.fill_diagonal, but allows for kth diagonals as well. This solution was borrowed from http://stackoverflow.com/questions/9958577/changing-the-values-of-the-diagonal-of-a-matrix-in-numpy
- cooltools.lib.numutils.slice_sorted(arr, lo, hi)[source]
Get the subset of a sorted array with values >=lo and <hi. A faster version of arr[(arr>=lo) & (arr<hi)]
- cooltools.lib.numutils.stochastic_sd(arr, n=10000, seed=0)[source]
Estimate the standard deviation of an array by considering only the subset of its elements.
- Parameters
n (int) – The number of elements to consider. If the array contains fewer elements, use all.
seed (int) – The seed for the random number generator.
- cooltools.lib.numutils.weighted_groupby_mean(df, group_by, weigh_by, mode='mean')[source]
Weighted mean, std, and std in log space for a dataframe.groupby
- Parameters
df (dataframe) – Dataframe to groupby
group_by (str or list) – Columns to group by
weight_by (str) – Column to use as weights
mode ("mean", "std" or "logstd") – Do the weighted mean, the weighted standard deviaton, or the weighted std in log-space from the mean-log value (useful for P(s) etc.)
- cooltools.lib.numutils.zoom_array(in_array, final_shape, same_sum=False, zoom_function=functools.partial(<Mock name='mock.zoom' id='139638368254656'>, order=1), **zoom_kwargs)[source]
Rescale an array or image.
Normally, one can use scipy.ndimage.zoom to do array/image rescaling. However, scipy.ndimage.zoom does not coarsegrain images well. It basically takes nearest neighbor, rather than averaging all the pixels, when coarsegraining arrays. This increases noise. Photoshop doesn’t do that, and performs some smart interpolation-averaging instead.
If you were to coarsegrain an array by an integer factor, e.g. 100x100 -> 25x25, you just need to do block-averaging, that’s easy, and it reduces noise. But what if you want to coarsegrain 100x100 -> 30x30?
Then my friend you are in trouble. But this function will help you. This function will blow up your 100x100 array to a 120x120 array using scipy.ndimage zoom Then it will coarsegrain a 120x120 array by block-averaging in 4x4 chunks.
It will do it independently for each dimension, so if you want a 100x100 array to become a 60x120 array, it will blow up the first and the second dimension to 120, and then block-average only the first dimension.
(Copied from mirnylib.numutils)
- Parameters
in_array (ndarray) – n-dimensional numpy array (1D also works)
final_shape (shape tuple) – resulting shape of an array
same_sum (bool, optional) – Preserve a sum of the array, rather than values. By default, values are preserved
zoom_function (callable) – By default, scipy.ndimage.zoom with order=1. You can plug your own.
**zoom_kwargs – Options to pass to zoomFunction.
- Returns
rescaled (ndarray) – Rescaled version of in_array
- cooltools.lib.peaks.find_peak_prominence(arr, max_dist=None)[source]
Find the local maxima of an array and their prominence. The prominence of a peak is defined as the maximal difference between the height of the peak and the lowest point in the range until a higher peak.
- Parameters
arr (array_like) –
max_dist (int) – If specified, the distance to the adjacent higher peaks is limited by max_dist.
- Returns
loc_max_poss (numpy.array) – The positions of local maxima of a given array.
proms (numpy.array) – The prominence of the detected maxima.
- cooltools.lib.peaks.find_peak_prominence_iterative(arr, min_prom=None, max_prom=None, steps_prom=1000, log_space_proms=True, min_n_peak_pairs=5)[source]
Finds the minima/maxima of an array using the peakdet algorithm at different values of the threshold prominence. For each location, returns the maximal threshold prominence at which it is called as a minimum/maximum.
Note that this function is inferior in every aspect to find_peak_prominence. We keep it for testing purposes and will remove in the future.
- Parameters
arr (array_like) –
min_prom (float) – The minimal and the maximal values of prominence to probe. If None, these values are inferred as the minimal and the maximal non-zero difference between any two elements of v.
max_prom (float) – The minimal and the maximal values of prominence to probe. If None, these values are inferred as the minimal and the maximal non-zero difference between any two elements of v.
steps_prom (int) – The number of threshold prominence values to probe in the range between min_prom and max_prom.
log_space_proms (bool) – If True, probe logarithmically spaced values of the threshold prominence in the range between min_prom and max_prom.
min_n_peak_pairs (int) – If the number of detected minima/maxima at a certain threshold prominence is < min_n_peak_pairs, the detected peaks are ignored.
- Returns
minproms, maxproms (numpy.array) – The prominence of detected minima and maxima.
- cooltools.lib.peaks.peakdet(arr, min_prominence)[source]
Detect local peaks in an array. Finds a sequence of minima and maxima such that the two consecutive extrema have a value difference (i.e. a prominence) >= min_prominence. This is analogous to the definition of prominence in topography: https://en.wikipedia.org/wiki/Topographic_prominence
The original peakdet algorithm was designed by Eli Billauer and described in http://billauer.co.il/peakdet.html (v. 3.4.05, Explicitly not copyrighted). This function is released to the public domain; Any use is allowed. The Python implementation was published by endolith on Github: https://gist.github.com/endolith/250860 .
Here, we use the endolith’s implementation with minimal to none modifications to the algorithm, but with significant changes in the interface and the documentation
- Parameters
arr (array_like) –
min_prominence (float) – The minimal prominence of detected extrema.
- Returns
maxidxs, minidx (numpy.array) – The indices of the maxima and minima in arr.
Migrated from mirnylib.plotting.
cooltools.api.coverage module
- cooltools.api.coverage.coverage(clr, ignore_diags=None, chunksize=10000000, use_lock=False, clr_weight_name=None, store=False, store_prefix='cov', nproc=1, map_functor=<class 'map'>)[source]
Calculate the sums of cis and genome-wide contacts (aka coverage aka marginals) for a sparse Hi-C contact map in Cooler HDF5 format. Note that for raw coverage (i.e. clr_weight_name=None) the sum(tot_cov) from this function is two times the number of reads contributing to the cooler, as each side contributes to the coverage.
- Parameters
clr (cooler.Cooler) – Cooler object
ignore_diags (int, optional) – Drop elements occurring on the first
ignore_diagsdiagonals of the matrix (including the main diagonal). If None, equals the number of diagonals ignored during IC balancing.chunksize (int, optional) – Split the contact matrix pixel records into equally sized chunks to save memory and/or parallelize. Default is 10^7
clr_weight_name (str) – Name of the weight column. Specify to calculate coverage of balanced cooler.
store (bool, optional) – If True, store the results in the input cooler file when finished. If clr_weight_name=None, also stores total cis counts in the cooler info. Default is False.
store_prefix (str, optional) – Name prefix of the columns of the bin table to save cis and total coverages. Will add suffixes _cis and _tot, as well as _raw in the default case or _clr_weight_name if specified.
nproc (int, optional) – How many processes to use for calculation. Ignored if map_functor is passed.
map_functor (callable, optional) – Map function to dispatch the matrix chunks to workers. If left unspecified, pool_decorator applies the following defaults: if nproc>1 this defaults to multiprocess.Pool; If nproc=1 this defaults the builtin map.
- Returns
cis_cov (1D array, whose shape is the number of bins in
h5. Vector of bin sums in cis.)tot_cov (1D array, whose shape is the number of bins in
h5. Vector of bin sums.)
cooltools.api.directionality module
- cooltools.api.directionality.directionality(clr, window_bp=100000, balance='weight', min_dist_bad_bin=2, ignore_diags=None, chromosomes=None)[source]
Calculate the diamond insulation scores and call insulating boundaries.
- Parameters
clr (cooler.Cooler) – A cooler with balanced Hi-C data.
window_bp (int) – The size of the sliding diamond window used to calculate the insulation score.
min_dist_bad_bin (int) – The minimal allowed distance to a bad bin. Do not calculate insulation scores for bins having a bad bin closer than this distance.
ignore_diags (int) – The number of diagonals to ignore. If None, equals the number of diagonals ignored during IC balancing.
- Returns
ins_table (pandas.DataFrame) – A table containing the insulation scores of the genomic bins and the insulating boundary strengths.
cooltools.api.dotfinder module
Collection of functions related to dot-calling
The main user-facing API function is:
dots(
clr,
expected,
expected_value_col="balanced.avg",
clr_weight_name="weight",
view_df=None,
kernels=None,
max_loci_separation=10_000_000,
max_nans_tolerated=1,
n_lambda_bins=40,
lambda_bin_fdr=0.1,
clustering_radius=20_000,
cluster_filtering=None,
tile_size=5_000_000,
nproc=1,
)
This function implements HiCCUPS-style dot calling, but enables user-specified modifications at multiple steps. The current implementation makes two passes over the input data, first to create a histogram of pixel enrichment values, and second to extract significantly enriched pixels.
The function starts with compatibility verifications
Recommendation or verification for kernels is done next. Custom kernels must satisfy properties including: square shape, equal sizes, odd sizes, zeros in the middle, etc. By default, HiCCUPS-style kernels are recommended based on the binsize.
Lambda bins are defined for multiple hypothesis testing separately for different value ranges of the locally adjusted expected. Currently, log-binned lambda-bins are hardcoded using a pre-defined BASE of 2^(1/3). n_lambda_bins controls the total number of bins. for the clr, expected and view of interest.
Genomic regions in the specified view`(all chromosomes by default) are split into smaller tiles of size `tile_size.
scoring_and_histogramming_step() is performed independently on the genomic tiles. In this step, locally adjusted expected is calculated using convolution kernels for each pixel in the tile. All surveyed pixels are histogrammed according to their adjusted expected and raw observed counts. Locally adjusted expected is not stored in memory.
Chunks of histograms are aggregated together and a modified BH-FDR procedure is applied to the result in determine_thresholds(). This returns thresholds for statistical significance in each lambda-bin (for observed counts), along with the adjusted p-values (q-values).
Calculated thresholds are used to extract statistically significant pixels in scoring_and_extraction_step(). Because locally adjusted expected is not stored in memory, it is re-caluclated during this step, which makes it computationally intensive. Locally adjusted expected values are required in order to apply different thresholds of significance depending on the lambda-bin.
Returned filtered pixels, or ‘dots’, are significantly enriched relative to their locally adjusted expecteds and thus have potential biological interest. Dots are further annotated with their genomic coordinates and q-values (adjusted p-values) for all applied kernels.
All further steps perform optional post-processing on called dots
enriched pixels that are within clustering_radius of each other are clustered together and the brightest one is selected as the representative position of a dot.
cluster-representatives along with “singletons” (enriched pixels that are not part of any cluster) can be subjected to further empirical enrichment filtering in cluster_filtering_hiccups(). This both requires clustered dots exceed prescribed enrichment thresholds relative to their local neighborhoods and that singletons pass an even more stringent q-value threshold.
- cooltools.api.dotfinder.adjusted_exp_name(kernel_name)
- cooltools.api.dotfinder.annotate_pixels_with_qvalues(pixels_df, qvalues, obs_raw_name='count')[source]
Add columns with the qvalues to a DataFrame of scored pixels
- Parameters
pixels_df (pandas.DataFrame) – a DataFrame with pixel coordinates that must have at least 2 columns named ‘bin1_id’ and ‘bin2_id’, where first is pixels’s row and the second is pixel’s column index.
qvalues (dict of DataFrames) – A dictionary with keys being kernel names and values DataFrames storing q-values for each observed count values in each lambda- bin. Colunms are Intervals defined by ‘ledges’ boundaries. Rows corresponding to a range of observed count values.
obs_raw_name (str) – Name of the column/field that carry number of counts per pixel, i.e. observed raw counts.
- Returns
pixels_qvalue_df (pandas.DataFrame) – DataFrame of pixels with additional columns la_exp.{k}.qval, storing q-values (adjusted p-values) corresponding to the count value of a pixel, its kernel, and a lambda-bin it belongs to.
- cooltools.api.dotfinder.clust_2D_pixels(pixels_df, threshold_cluster=2, bin1_id_name='bin1_id', bin2_id_name='bin2_id', clust_label_name='c_label', clust_size_name='c_size')[source]
Group significant pixels by proximity using Birch clustering. We use “n_clusters=None”, which implies no AgglomerativeClustering, and thus simply reporting “blobs” of pixels of radii <=”threshold_cluster” along with corresponding blob-centroids as well.
- Parameters
pixels_df (pandas.DataFrame) – a DataFrame with pixel coordinates that must have at least 2 columns named ‘bin1_id’ and ‘bin2_id’, where first is pixels’s row and the second is pixel’s column index.
threshold_cluster (int) – clustering radius for Birch clustering derived from ~40kb radius of clustering and bin size.
bin1_id_name (str) – Name of the 1st coordinate (row index) in ‘pixel_df’, by default ‘bin1_id’. ‘start1/end1’ could be usefull as well.
bin2_id_name (str) – Name of the 2nd coordinate (column index) in ‘pixel_df’, by default ‘bin2_id’. ‘start2/end2’ could be usefull as well.
clust_label_name (str) – Name of the cluster of pixels label. “c_label” by default.
clust_size_name (str) – Name of the cluster of pixels size. “c_size” by default.
- Returns
peak_tmp (pandas.DataFrame) – DataFrame with the following columns: [c+bin1_id_name, c+bin2_id_name, clust_label_name, clust_size_name] row/col (bin1/bin2) are coordinates of centroids, label and sizes are unique pixel-cluster labels and their corresponding sizes.
- cooltools.api.dotfinder.cluster_filtering_hiccups(centroids, obs_raw_name='count', enrichment_factor_vh=1.5, enrichment_factor_d_and_ll=1.75, enrichment_factor_d_or_ll=2.0, FDR_orphan_threshold=0.02)[source]
Centroids of enriched pixels can be filtered to further minimize the amount of false-positive dot-calls.
First, centroids are filtered on enrichment relative to the locally-adjusted expected for the “donut”, “lowleft”, “vertical”, and “horizontal” kernels. Additionally, singleton pixels (i.e. pixels that do not belong to a cluster) are filtered based on a combined q-values for all kernels. This empirical filtering approach was developed in Rao et al 2014 and results in a conservative dot-calls with the low rate of false-positive calls.
- Parameters
centroids (pd.DataFrame) – DataFrame that stores enriched and clustered pixels.
obs_raw_name (str) – name of the column with raw observed pixel counts
enrichment_factor_vh (float) – minimal enrichment factor for pixels relative to both “vertical” and “horizontal” kernel.
enrichment_factor_d_and_ll (float) – minimal enrichment factor for pixels relative to both “donut” and “lowleft” kernels.
enrichment_factor_d_or_ll (float) – minimal enrichment factor for pixels relative to either “donut” or” “lowleft” kenels.
FDR_orphan_threshold (float) – minimal combined q-value for singleton pixels.
- Returns
filtered_centroids (pd.DataFrame) – filtered dot-calls
- cooltools.api.dotfinder.clustering_step(scored_df, dots_clustering_radius, assigned_regions_name='region', obs_raw_name='count')[source]
Group together adjacent significant pixels into clusters after the lambda-binning multiple hypothesis testing by iterating over assigned regions and calling clust_2D_pixels.
- Parameters
scored_df (pandas.DataFrame) – DataFrame with enriched pixels that are ready to be clustered and are annotated with their genomic coordinates.
dots_clustering_radius (int) – Birch-clustering threshold.
assigned_regions_name (str | None) – Name of the column in scored_df to use for grouping pixels before clustering. When None, full chromosome clustering is done.
obs_raw_name (str) – name of the column with raw observed pixel counts
- Returns
centroids (pandas.DataFrame) – Pixels from ‘scored_df’ annotated with clustering information.
Notes
‘dots_clustering_radius’ in Birch clustering algorithm corresponds to a double the clustering radius in the “greedy”-clustering used in HiCCUPS
- cooltools.api.dotfinder.determine_thresholds(gw_hist, fdr)[source]
given a ‘gw_hist’ histogram of observed counts for each lambda-bin and for each kernel-type, and also given a FDR, calculate q-values for each observed count value in each lambda-bin for each kernel-type.
- Parameters
gw_hist_kernels (dict) – dictionary {kernel_name : 2D_hist}, where ‘2D_hist’ is a pd.DataFrame
fdr (float) – False Discovery Rate level
- Returns
threshold_df (dict) – each threshold_df[k] is a Series indexed by la_exp intervals (IntervalIndex) and it is all we need to extract “good” pixels from each chunk …
qvalues (dict) – A dictionary with keys being kernel names and values pandas.DataFrames storing q-values: each column corresponds to a lambda-bin, while rows correspond to observed pixels values.
- cooltools.api.dotfinder.dots(clr, expected, expected_value_col='balanced.avg', clr_weight_name='weight', view_df=None, kernels=None, max_loci_separation=10000000, max_nans_tolerated=1, n_lambda_bins=40, lambda_bin_fdr=0.1, clustering_radius=20000, cluster_filtering=None, tile_size=5000000, nproc=1)[source]
Call dots on a cooler {clr}, using {expected} defined in regions specified in {view_df}.
All convolution kernels specified in {kernels} will be all applied to the {clr}, and statistical testing will be performed separately for each kernel. A convolutional kernel is a small squared matrix (e.g. 7x7) of zeros and ones that defines a “mask” to extract local expected around each pixel. Since the enrichment is calculated relative to the central pixel, kernel width should be an odd number >=3.
- Parameters
clr (cooler.Cooler) – A cooler with balanced Hi-C data.
expected (DataFrame in expected format) – Diagonal summary statistics for each chromosome, and name of the column with the values of expected to use.
expected_value_col (str) – Name of the column in expected that holds the values of expected
clr_weight_name (str) – Name of the column in the clr.bins to use as balancing weights. Using raw unbalanced data is not supported for dot-calling.
view_df (viewframe) – Viewframe with genomic regions, at the moment the view has to match the view used for generating expected. If None, generate from the cooler.
kernels ({ str:np.ndarray } | None) – A dictionary of convolution kernels to be used for calculating locally adjusted expected. If None the default kernels from HiCCUPS are going to be recommended based on the resolution of the cooler.
max_loci_separation (int) – Miaximum loci separation for dot-calling, i.e., do not call dots for loci that are further than max_loci_separation basepair apart. default 10Mb.
max_nans_tolerated (int) – Maximum number of NaNs tolerated in a footprint of every used kernel Adjust with caution, as large max_nans_tolerated, might lead to artifacts in pixels scoring.
n_lambda_bins (int) – Number of log-spaced bins, where FDR-testing will be performed independently. TODO: generate lambda-bins on the fly based on the dynamic range of the data (i.e. maximum pixel count)
lambda_bin_fdr (float) – False discovery rate (FDR) for multiple hypothesis testing BH-FDR procedure, applied per lambda bin.
clustering_radius (None | int) – Cluster enriched pixels with a given radius. “Brightest” pixels in each group will be reported as the final dot-calls. If None, no clustering is performed.
cluster_filtering (bool) – whether to apply additional filtering to centroids after clustering, using cluster_filtering_hiccups()
tile_size (int) – Tile size for the Hi-C heatmap tiling. Typically on order of several mega-bases, and <= max_loci_separation. Controls tradeoff between memory consumption and speed of execution.
nproc (int) – Number of processes to use for multiprocessing.
- Returns
dots (pandas.DataFrame) – BEDPE-style dataFrame with genomic coordinates of called dots and additional annotations.
Notes
‘clustering_radius’ in Birch clustering algorithm corresponds to a double the clustering radius in the “greedy”-clustering used in HiCCUPS (to be tested).
TODO describe sequence of processing steps
- cooltools.api.dotfinder.extract_scored_pixels(scored_df, thresholds, ledges, obs_raw_name='count')[source]
Implementation of HiCCUPS-like lambda-binning statistical procedure. Use FDR thresholds for different “classes” of hypothesis (classified by their locally-adjusted expected (la_exp) scores), in order to extract “enriched” pixels.
- Parameters
scored_df (pd.DataFrame) – A table with the scoring information for a group of pixels.
thresholds (dict) – A dictionary {kernel_name : lambda_thresholds}, where ‘lambda_thresholds’ are pd.Series with FDR thresholds indexed by lambda-bin intervals
ledges (ndarray) – An ndarray with bin lambda-edges for groupping locally adjusted expecteds, i.e., classifying statistical hypothesis into lambda-bins. Left-most bin (-inf, 1], and right-most one (value,+inf].
obs_raw_name (str) – Name of the column/field with number of counts per pixel, i.e. observed raw counts.
- Returns
scored_df_slice (pandas.DataFrame) – Filtered DataFrame of pixels that satisfy thresholds.
- cooltools.api.dotfinder.generate_tiles_diag_band(clr, view_df, pad_size, tile_size, band_to_cover)[source]
A generator yielding corrdinates of heatmap tiles that are needed to cover the requested band_to_cover around diagonal. Each tile is “padded” with the pad of size ‘pad_size’ to allow for convolution near the boundary of a tile.
- Parameters
clr (cooler) – Cooler object to use to extract chromosome extents.
view_df (viewframe) – Viewframe with genomic regions to process, chrom, start, end, name.
pad_size (int) – Size of padding around each tile. Typically the outer size of the kernel.
tile_size (int) – Size of the heatmap tile.
band_to_cover (int) – Size of the diagonal band to be covered by the generated tiles. Typically correspond to the max_loci_separation for called dots.
- Returns
tile_coords (tuple) – Generator of tile coordinates, i.e. tuples of three: (region_name, tile_span_i, tile_span_j), where ‘tile_span_i/j’ each is a tuple of bin ids (bin_start, bin_end).
- cooltools.api.dotfinder.get_adjusted_expected_tile_some_nans(origin_ij, observed, expected, bal_weights, kernels)[source]
Get locally adjusted expected for a collection of local-filters (kernels).
Such locally adjusted expected, ‘Ek’ for a given kernel, can serve as a baseline for deciding whether a given pixel is enriched enough to call it a feature (dot-loop, flare, etc.) in a downstream analysis.
For every pixel of interest [i,j], locally adjusted expected is a product of a global expected in that pixel E_bal[i,j] and an enrichment of local environ- ment of the pixel, described with a given kernel:
KERNEL[i,j](O_bal) Ek_bal[i,j] = E_bal[i,j]* ------------------ KERNEL[i,j](E_bal)
where KERNEL[i,j](X) is a result of convolution between the kernel and a slice of matrix X centered around (i,j). See link below for details: https://en.wikipedia.org/wiki/Kernel_(image_processing)
Returned values for observed and all expecteds are rescaled back to raw-counts, for the sake of downstream statistical analysis, which is using Poisson test to decide is a given pixel is enriched. (comparison between balanced values using Poisson- test is intractable):
KERNEL[i,j](O_bal) Ek_raw[i,j] = E_raw[i,j]* ------------------ , KERNEL[i,j](E_bal)
where E_raw[i,j] is:
1 1 -------------- * -------------- * E_bal[i,j] bal_weights[i] bal_weights[j]
- Parameters
origin_ij ((int,int) tuple) – tuple of interegers that specify the location of an observed matrix slice. Measured in bins, not in nucleotides.
observed (numpy.ndarray) – square symmetrical dense-matrix that contains balanced observed O_bal
expected (numpy.ndarray) – square symmetrical dense-matrix that contains expected, calculated based on balanced observed: E_bal.
bal_weights (numpy.ndarray or (numpy.ndarray, numpy.ndarray)) – 1D vector used to turn raw observed into balanced observed for a slice of a matrix with the origin_ij on the diagonal; and a tuple/list of a couple of 1D arrays in case it is a slice with an arbitrary origin_ij.
kernels (dict of (str, numpy.ndarray)) – dictionary of kernels/masks to perform convolution of the heatmap. Kernels describe the local environment, and used to estimate baseline for finding enriched/prominent peaks. Peak must be enriched with respect to all local environments (all kernels), to be considered significant. Dictionay keys must contain names for each kernel. Note, scipy.ndimage.convolve first flips kernel and only then applies it to matrix.
- Returns
peaks_df (pandas.DataFrame) – DataFrame with the results of locally adjusted calculations for every kernel for a given slice of input matrix.
Notes
- Reported columns:
bin1_id - bin1_id index (row), adjusted to tile_start_i bin2_id - bin bin2_id index, adjusted to tile_start_j la_exp - locally adjusted expected (for each kernel) la_nan - number of NaNs around (each kernel’s footprint) exp.raw - global expected, rescaled to raw-counts obs.raw(counts) - observed values in raw-counts.
Depending on the intial tiling of the interaction matrix, concatened peaks_df may require “deduplication”, as some pixels can be evaluated in several tiles (e.g. near the tile edges). Default tilitng in the dots functions, should avoid this problem.
- cooltools.api.dotfinder.histogram_scored_pixels(scored_df, kernels, ledges, obs_raw_name='count')[source]
An attempt to implement HiCCUPS-like lambda-binning statistical procedure. This function aims at building up a histogram of locally adjusted expected scores for groups of characterized pixels.
Such histograms are subsequently used to compute FDR thresholds for different “classes” of hypothesis (classified by their locally-adjusted expected (la_exp)).
- Parameters
scored_df (pd.DataFrame) – A table with the scoring information for a group of pixels.
kernels (dict) – A dictionary with keys being kernels names and values being ndarrays representing those kernels.
ledges (ndarray) – An ndarray with bin lambda-edges for groupping locally adjusted expecteds, i.e., classifying statistical hypothesis into lambda-bins. Left-most bin (-inf, 1], and right-most one (value,+inf].
obs_raw_name (str) – Name of the column/field that carry number of counts per pixel, i.e. observed raw counts.
- Returns
hists (dict of pandas.DataFrame) – A dictionary of pandas.DataFrame with lambda/observed 2D histogram for every kernel-type.
Notes
returning histograms corresponding to the chunks of scored pixels.
- cooltools.api.dotfinder.is_compatible_kernels(kernels, binsize, max_nans_tolerated)[source]
- TODO implement checks for kernels:
matrices are of the same size
they should be squared (too restrictive ? maybe pad with 0 as needed)
dimensions are odd, to have a center pixel to refer to
they can be turned into int 1/0 ones (too restrictive ? allow weighted kernels ?)
the central pixel should be zero perhaps (unless weights are allowed 4sure)
maybe introduce an upper limit to the size - to avoid crazy long calculations
check relative to the binsize maybe ? what’s the criteria ?
- cooltools.api.dotfinder.nans_inkernel_name(kernel_name)
- cooltools.api.dotfinder.recommend_kernels(binsize)[source]
Return a recommended set of convolution kernels for dot-calling based on the resolution, or binsize, of the input data.
This function currently recommends the four kernels used in the HiCCUPS method: donut, horizontal, vertical, lowerleft. Kernels are recommended for resolutions near 5 kb, 10 kb, and 25 kb. Dots are not typically visible at lower resolutions (binsize >28kb) and the majority of datasets are too sparse for dot-calling at very high resolutions (<4kb). Given this, default kernels are not recommended for resolutions outside this range.
- Parameters
binsize (integer) – binsize of the provided cooler
- Returns
kernels ({str:ndarray}) – dictionary of convolution kernels as ndarrays, with their names as keys.
- cooltools.api.dotfinder.score_tile(tile_cij, clr, expected_indexed, expected_value_col, clr_weight_name, kernels, max_nans_tolerated, band_to_cover)[source]
The main working function that given a tile of a heatmap, applies kernels to perform convolution to calculate locally-adjusted expected and then calculates a p-value for every meaningfull pixel against these locally-adjusted expected (la_exp) values.
- Parameters
tile_cij (tuple) – Tuple of 3: region name, tile span row-wise, tile span column-wise: (region, tile_span_i, tile_span_j), where tile_span_i = (start_i, end_i), and tile_span_j = (start_j, end_j).
clr (cooler) – Cooler object to use to extract Hi-C heatmap data.
expected_indexed (pandas.DataFrame) – DataFrame with cis-expected, indexed with ‘region1’, ‘region2’, ‘dist’.
expected_value_col (str) – Name of a value column in expected DataFrame
clr_weight_name (str) – Name of a value column with balancing weights in a cooler.bins() DataFrame. Typically ‘weight’.
kernels (dict) – A dictionary with keys being kernels names and values being ndarrays representing those kernels.
max_nans_tolerated (int) – Number of NaNs tolerated in a footprint of every kernel.
band_to_cover (int) – Results would be stored only for pixels connecting loci closer than ‘band_to_cover’.
- Returns
res_df (pandas.DataFrame) – results: annotated pixels with calculated locally adjusted expected for every kernels, observed, precalculated pvalues, number of NaNs in footprint of every kernels, all of that in a form of an annotated pixels DataFrame for eligible pixels of a given tile.
- cooltools.api.dotfinder.scoring_and_extraction_step(clr, expected_indexed, expected_value_col, clr_weight_name, tiles, kernels, ledges, thresholds, max_nans_tolerated, loci_separation_bins, nproc, bin1_id_name='bin1_id', bin2_id_name='bin2_id', map_functor=<class 'map'>)[source]
This implements the 2nd step of the lambda-binning scoring procedure, extracting pixels that are FDR compliant.
In short, this combines scoring with with extraction into a single pipeline of per-chunk operations/transforms.
- cooltools.api.dotfinder.scoring_and_histogramming_step(clr, expected_indexed, expected_value_col, clr_weight_name, tiles, kernels, ledges, max_nans_tolerated, loci_separation_bins, nproc, map_functor=<class 'map'>)[source]
This implements the 1st step of the lambda-binning scoring procedure - histogramming.
In short, this pipes a scoring operation together with histogramming into a single pipeline of per-chunk operations/transforms.
- cooltools.api.dotfinder.tile_square_matrix(matrix_size, offset, tile_size, pad=0)[source]
Generate a stream of coordinates of tiles that cover a matrix of a given size. Matrix has to be square, on-digaonal one: e.g. corresponding to a chromosome or a chromosomal arm.
- Parameters
matrix_size (int) – Size of a squared matrix
offset (int) – Offset coordinates of generated tiles by ‘offset’
tile_size (int) – Requested size of the tiles. Tiles near the right and botoom edges could be rectangular and smaller then ‘tile_size’
pad (int) – Small padding around each tile to be included in the yielded coordinates.
- Yields
Pairs of indices/coordinates of every tile ((start_i, end_i), (start_j, end_j))
Notes
Generated tiles coordinates [start_i,end_i) , [start_i,end_i) can be used to fetch heatmap tiles from cooler: >>> clr.matrix()[start_i:end_i, start_j:end_j]
‘offset’ is useful when a given matrix is part of a larger matrix (a given chromosome or arm), and thus all coordinated needs to be offset to get absolute coordinates.
Tiles are non-overlapping (pad=0), but tiles near the right and bottom edges could be rectangular:
… *
cooltools.api.eigdecomp module
- cooltools.api.eigdecomp.cis_eig(A, n_eigs=3, phasing_track=None, ignore_diags=2, clip_percentile=0, sort_metric=None)[source]
Compute compartment eigenvector on a dense cis matrix.
Note that the amplitude of compartment eigenvectors is weighted by their corresponding eigenvalue
- Parameters
A (2D array) – balanced dense contact matrix
n_eigs (int) – number of eigenvectors to compute
phasing_track (1D array, optional) – if provided, eigenvectors are flipped to achieve a positive correlation with phasing_track.
ignore_diags (int) – the number of diagonals to ignore
clip_percentile (float) – if >0 and <100, clip pixels with diagonal-normalized values higher than the specified percentile of matrix-wide values.
sort_metric (str) – If provided, re-sort eigenvecs and eigvals in the order of decreasing correlation between phasing_track and eigenvector, using the specified measure of correlation. Possible values: ‘pearsonr’ - sort by decreasing Pearson correlation. ‘var_explained’ - sort by decreasing absolute amount of variation in eigvecs explained by phasing_track (i.e. R^2 * var(eigvec)) ‘MAD_explained’ - sort by decreasing absolute amount of Median Absolute Deviation from the median of eigvecs explained by phasing_track (i.e. COMED(eigvec, phasing_track) * MAD(eigvec)). ‘spearmanr’ - sort by decreasing Spearman correlation. This option is designed to report the most “biologically” informative eigenvectors first, and prevent eigenvector swapping caused by translocations. In reality, however, sometimes it shows poor performance and may lead to reporting of non-informative eigenvectors. Off by default.
- Returns
eigenvalues, eigenvectors
.. note:: ALWAYS check your EVs by eye. The first one occasionally does – not reflect the compartment structure, but instead describes chromosomal arms or translocation blowouts.
- cooltools.api.eigdecomp.eigs_cis(clr, phasing_track=None, view_df=None, n_eigs=3, clr_weight_name='weight', ignore_diags=None, clip_percentile=99.9, sort_metric=None, map=<class 'map'>)[source]
Compute compartment eigenvector for a given cooler clr in a number of symmetric intra chromosomal regions defined in view_df (cis-regions), or for each chromosome.
Note that the amplitude of compartment eigenvectors is weighted by their corresponding eigenvalue. Eigenvectors can be oriented by passing a binned phasing_track with the same resolution as the cooler.
- Parameters
clr (cooler) – cooler object to fetch data from
phasing_track (DataFrame) – binned track with the same resolution as cooler bins, the fourth column is used to phase the eigenvectors, flipping them to achieve a positive correlation.
view_df (iterable or DataFrame, optional) – if provided, eigenvectors are calculated for the regions of the view only, otherwise chromosome-wide eigenvectors are computed, for chromosomes specified in phasing_track.
n_eigs (int) – number of eigenvectors to compute
clr_weight_name (str) – name of the column with balancing weights to be used.
ignore_diags (int, optional) – the number of diagonals to ignore. Derived from cooler metadata if not specified.
clip_percentile (float) – if >0 and <100, clip pixels with diagonal-normalized values higher than the specified percentile of matrix-wide values.
sort_metric (str) – If provided, re-sort eigenvecs and eigvals in the order of decreasing correlation between phasing_track and eigenvector, using the specified measure of correlation. Possible values: ‘pearsonr’ - sort by decreasing Pearson correlation. ‘var_explained’ - sort by decreasing absolute amount of variation in eigvecs explained by phasing_track (i.e. R^2 * var(eigvec)) ‘MAD_explained’ - sort by decreasing absolute amount of Median Absolute Deviation from the median of eigvecs explained by phasing_track (i.e. COMED(eigvec, phasing_track) * MAD(eigvec)). ‘spearmanr’ - sort by decreasing Spearman correlation. This option is designed to report the most “biologically” informative eigenvectors first, and prevent eigenvector swapping caused by translocations. In reality, however, sometimes it shows poor performance and may lead to reporting of non-informative eigenvectors. Off by default.
map (callable, optional) – Map functor implementation.
- Returns
eigvals, eigvec_table -> DataFrames with eigenvalues for each region and
a table of eigenvectors filled in the bins table.
.. note:: ALWAYS check your EVs by eye. The first one occasionally does – not reflect the compartment structure, but instead describes chromosomal arms or translocation blowouts. Possible mitigations: employ view_df (e.g. arms) to avoid issues with chromosomal arms, consider blacklisting regions with translocations during balancing.
- cooltools.api.eigdecomp.eigs_trans(clr, phasing_track=None, n_eigs=3, partition=None, clr_weight_name='weight', sort_metric=None, **kwargs)[source]
- cooltools.api.eigdecomp.trans_eig(A, partition, n_eigs=3, perc_top=99.95, perc_bottom=1, phasing_track=None, sort_metric=False)[source]
Compute compartmentalization eigenvectors on trans contact data
- Parameters
A (2D array) – balanced whole genome contact matrix
partition (sequence of int) – bin offset of each contiguous region to treat separately (e.g., chromosomes or chromosome arms)
n_eigs (int) – number of eigenvectors to compute; default = 3
perc_top (float (percentile)) – filter - clip trans blowout contacts above this cutoff; default = 99.95
perc_bottom (float (percentile)) – filter - remove bins with trans coverage below this cutoff; default=1
phasing_track (1D array, optional) – if provided, eigenvectors are flipped to achieve a positive correlation with phasing_track.
sort_metric (str) – If provided, re-sort eigenvecs and eigvals in the order of decreasing correlation between phasing_track and eigenvector, using the specified measure of correlation. Possible values: ‘pearsonr’ - sort by decreasing Pearson correlation. ‘var_explained’ - sort by decreasing absolute amount of variation in eigvecs explained by phasing_track (i.e. R^2 * var(eigvec)) ‘MAD_explained’ - sort by decreasing absolute amount of Median Absolute Deviation from the median of eigvecs explained by phasing_track (i.e. COMED(eigvec, phasing_track) * MAD(eigvec)). ‘spearmanr’ - sort by decreasing Spearman correlation. This option is designed to report the most “biologically” informative eigenvectors first, and prevent eigenvector swapping caused by translocations. In reality, however, sometimes it shows poor performance and may lead to reporting of non-informative eigenvectors. Off by default.
- Returns
eigenvalues, eigenvectors
.. note:: ALWAYS check your EVs by eye. The first one occasionally does – not reflect the compartment structure, but instead describes chromosomal arms or translocation blowouts.
cooltools.api.expected module
- cooltools.api.expected.blocksum_pairwise(clr, view_df, transforms={}, clr_weight_name='weight', chunksize=1000000, map=<class 'map'>)[source]
Summary statistics on rectangular blocks of all (trans-)pairwise combinations of genomic regions in the view_df (aka trans-expected).
Note
This is a special case of asymmetric block-level summary stats, that can be calculated very efficiently. Regions in view_df are assigned to pixels only once and pixels falling into a given asymmetric block i != j are summed up.
- Parameters
clr (cooler.Cooler) – Cooler object
view_df (viewframe) – view_df of regions defining blocks for summary calculations, has to be sorted according to the order of chromosomes in clr.
transforms (dict of str -> callable, optional) – Transformations to apply to pixels. The result will be assigned to a temporary column with the name given by the key. Callables take one argument: the current chunk of the (annotated) pixel dataframe.
clr_weight_name (str) – name of the balancing weight column in cooler bin-table used to count “bad” pixels per block. Set to None not ot mask “bad” pixels (raw data only).
chunksize (int, optional) – Size of pixel table chunks to process
map (callable, optional) – Map functor implementation.
- Returns
DataFrame with entries for each blocks (region1, region2, n_valid, count.sum)
- cooltools.api.expected.combine_binned_expected(binned_exp, binned_exp_slope=None, Pc_name='balanced.avg', der_smooth_function_combined=<function <lambda>>, spread_funcs='logstd', spread_funcs_slope='std', minmax_drop_bins=2, concat_original=False)[source]
Combines by-region log-binned expected and slopes into genome-wide averages, handling small chromosomes and “corners” in an optimal fashion, robust to outliers. Calculates spread of by-chromosome P(s) and slopes, also in an optimal fashion.
- Parameters
binned_exp (dataframe) – binned expected as outputed by logbin_expected
binned_exp_slope (dataframe or None) – If provided, estimates spread of slopes. Is necessary if concat_original is True
Pc_name (str) – Name of the column with the probability of contacts. Defaults to “balanced.avg”.
der_smooth_function_combined (callable) – A smoothing function for calculating slopes on combined data
spread_funcs ("minmax", "std", "logstd" or a function (see below)) – A way to estimate the spread of the P(s) curves between regions. * “minmax” - use the minimum/maximum of by-region P(s) * “std” - use weighted standard deviation of P(s) curves (may produce negative results) * “logstd” (recommended) weighted standard deviation in logspace (as seen on the plot)
spread_funcs_slope ("minmax", "std" or a funciton) – Similar to spread_func, but for slopes rather than P(s)
concat_original (bool (default = False)) – Append original dataframe, and put combined under region “combined”
- Returns
scal, slope_df
Notes
This function does not calculate errorbars. The spread is not the deviation of the mean, and rather is representative of variability between chromosomes.
Calculating errorbars/spread
Take all by-region P(s)
For “minmax”, remove the last var_drop_last_bins bins for each region (by default two. They are most noisy and would inflate the spread for the last points). Min/max are most susceptible to this.
Groupby P(s) by region
Apply spread_funcs to the pd.GroupBy object. Options are: * minimum and maximum (“minmax”), * weighted standard deviation (“std”), * weighted standard deviation in logspace (“logstd”, default) or two custom functions We do not remove the last bins for “std” / “logstd” because we are doing weighted standard deviation. Therefore, noisy “ends” of regions would contribute very little to this.
Append them to the P(s) for the same bin.
As a result, by for minmax, we do not estimate spread for the last two bins. This is because there are often very few chromosomal arms there, and different arm measurements are noisy. For other methods, we do estimate the spread there, and noisy last bins are taken care of by the weighted standard deviation. However, the spread in the last bins may be noisy, and may become a 0 if only one region is contributing to the last pixel.
- cooltools.api.expected.count_all_pixels_per_block(x, y)[source]
Calculate total number of pixels in a rectangular block
- Parameters
x (int) – block width in pixels
y (int) – block height in pixels
- Returns
number_of_pixels (int) – total number of pixels in a block
- cooltools.api.expected.count_all_pixels_per_diag(n)[source]
Total number of pixels on each upper diagonal of a square matrix.
- Parameters
n (int) – total number of bins (dimension of square matrix)
- Returns
dcount (1D array of length n) – dcount[d] == total number of pixels on diagonal d
- cooltools.api.expected.count_bad_pixels_per_block(x, y, bad_bins_x, bad_bins_y)[source]
Calculate number of “bad” pixels per rectangular block of a contact map
- Parameters
x (int) – block width in pixels
y (int) – block height in pixels
bad_bins_x (int) – number of bad bins on x-side
bad_bins_y (int) – number of bad bins on y-side
- Returns
number_of_pixes (int) – number of “bad” pixels in a block
- cooltools.api.expected.count_bad_pixels_per_diag(n, bad_bins)[source]
Efficiently count the number of bad pixels on each upper diagonal of a matrix assuming a sequence of bad bins forms a “grid” of invalid pixels.
Each bad bin bifurcates into two a row and column of bad pixels, so an upper bound on number of bad pixels per diagonal is 2*k, where k is the number of bad bins. For a given diagonal, we need to subtract from this upper estimate the contribution from rows/columns reaching “out-of-bounds” and the contribution of the intersection points of bad rows with bad columns that get double counted.
o : bad bin * : bad pixel x : intersection bad pixel $ : out of bounds bad pixel $ $ $ *--------------------------+ * * * * | * * * * | ** * * | o****x*****x***********|$ * * * | * * * | * * * | o******x***********|$ * * | * * | * * | * * | * * | ** | o***********|$ * | * |- Parameters
n (int) – total number of bins
bad_bins (1D array of int) – sorted array of bad bin indexes
- Returns
dcount (1D array of length n) – dcount[d] == number of bad pixels on diagonal d
- cooltools.api.expected.diagsum_from_array(A, counts=None, *, offset=0, ignore_diags=2, filter_counts=False, region_name=None)[source]
Calculates Open2C-formatted expected for a dense submatrix of a whole genome contact map.
- Parameters
A (2D array) – Normalized submatrix to calculate expected (
balanced.sum).counts (2D array or None, optional) – Corresponding raw contacts to populate
count.sum.offset (int or (int, int)) – i- and j- bin offsets of A relative to the parent matrix. If a single offset is provided it is applied to both axes.
ignore_diags (int, optional) – Number of initial diagonals to ignore.
filter_counts (bool, optional) – Apply the validity mask from balanced matrix to the raw one. Ignored when counts is None.
region_name (str or (str, str), optional) – A custom region name or pair of region names. If provided, region columns will be included in the output.
Notes
For regions that cross the main diagonal of the whole-genome contact map, the lower triangle “overhang” is ignored.
Examples
>>> A = clr.matrix()[:, :] # whole genome balanced >>> C = clr.matrix(balance=False)[:, :] # whole genome raw
Using only balanced data: >>> exp = diagsum_from_array(A)
Using balanced and raw counts: >>> exp1 = diagsum_from_array(A, C)
Using an off-diagonal submatrix >>> exp2 = diagsum_from_array(A[:50, 50:], offset=(0, 50))
- cooltools.api.expected.diagsum_pairwise(clr, view_df, transforms={}, clr_weight_name='weight', ignore_diags=2, chunksize=10000000, map=<class 'map'>)[source]
Intra-chromosomal diagonal summary statistics for asymmetric blocks of contact matrix defined as pairwise combinations of regions in “view_df.
Note
This is a special case of asymmetric diagonal summary statistic that is efficient and covers the most important practical case of inter-chromosomal arms “expected” calculation.
- Parameters
clr (cooler.Cooler) – Cooler object
view_df (viewframe) – view_df of regions for intra-chromosomal diagonal summation, has to be sorted according to the order of chromosomes in cooler.
transforms (dict of str -> callable, optional) – Transformations to apply to pixels. The result will be assigned to a temporary column with the name given by the key. Callables take one argument: the current chunk of the (annotated) pixel dataframe.
clr_weight_name (str) – name of the balancing weight vector used to count “bad” pixels per diagonal. Set to None not to mask “bad” pixels (raw data only).
chunksize (int, optional) – Size of pixel table chunks to process
map (callable, optional) – Map functor implementation.
- Returns
Dataframe of diagonal statistics for all intra-chromosomal blocks defined as
pairwise combinations of regions in the view
- cooltools.api.expected.diagsum_symm(clr, view_df, transforms={}, clr_weight_name='weight', ignore_diags=2, chunksize=10000000, map=<class 'map'>)[source]
Intra-chromosomal diagonal summary statistics.
- Parameters
clr (cooler.Cooler) – Cooler object
view_df (viewframe) – view_dfof regions for intra-chromosomal diagonal summation
transforms (dict of str -> callable, optional) – Transformations to apply to pixels. The result will be assigned to a temporary column with the name given by the key. Callables take one argument: the current chunk of the (annotated) pixel dataframe.
clr_weight_name (str) – name of the balancing weight vector used to count “bad” pixels per diagonal. Set to None not to mask “bad” pixels (raw data only).
chunksize (int, optional) – Size of pixel table chunks to process
ignore_diags (int, optional) – Number of intial diagonals to exclude from statistics
map (callable, optional) – Map functor implementation.
- Returns
Dataframe of diagonal statistics for all regions in the view
- cooltools.api.expected.expected_cis(clr, view_df=None, intra_only=True, smooth=True, aggregate_smoothed=True, smooth_sigma=0.1, clr_weight_name='weight', ignore_diags=2, chunksize=10000000, nproc=1, map_functor=<class 'map'>)[source]
Calculate average interaction frequencies as a function of genomic separation between pixels i.e. interaction decay with distance. Genomic separation aka “dist” is measured in the number of bins, and defined as an index of a diagonal on which pixels reside (bin1_id - bin2_id).
Average values are reported in the columns with names {}.avg, and they are calculated as a ratio between a corresponding sum {}.sum and the total number of “valid” pixels on the diagonal “n_valid”.
When balancing weights (clr_weight_name=None) are not applied to the data, there is no masking of bad bins performed.
- Parameters
clr (cooler.Cooler) – Cooler object
view_df (viewframe) – a collection of genomic intervals where expected is calculated otherwise expected is calculated for full chromosomes. view_df has to be sorted, when inter-regions expected is requested, i.e. intra_only is False.
intra_only (bool) – Return expected only for symmetric intra-regions defined by view_df, i.e. chromosomes, chromosomal-arms, intra-domains, etc. When False returns expected both for symmetric intra-regions and assymetric inter-regions.
smooth (bool) – Apply smoothing to cis-expected. Will be stored in an additional column
aggregate_smoothed (bool) – When smoothing, average over all regions, ignored without smoothing.
smooth_sigma (float) – Control smoothing with the standard deviation of the smoothing Gaussian kernel. Ignored without smoothing.
clr_weight_name (str or None) – Name of balancing weight column from the cooler to use. Use raw unbalanced data, when None.
ignore_diags (int, optional) – Number of intial diagonals to exclude results
chunksize (int, optional) – Size of pixel table chunks to process
nproc (int, optional) – How many processes to use for calculation. Ignored if map_functor is passed.
map_functor (callable, optional) – Map function to dispatch the matrix chunks to workers. If left unspecified, pool_decorator applies the following defaults: if nproc>1 this defaults to multiprocess.Pool; If nproc=1 this defaults the builtin map.
- Returns
DataFrame with summary statistic of every diagonal of every symmetric
or asymmetric block
Notes
When clr_weight_name=None, smooth=False, aggregate_smoothed=False, the minimum output DataFrame includes the following quantities (columns):
- dist:
Distance in bins.
- dist_bp:
Distance in basepairs.
- contact_freq:
The “most processed” contact frequency value. For example, if balanced & smoothing then this will return the balanced.avg.smooth.agg; if aggregated+smoothed, then balanced.avg.smooth.agg; if nothing then count.avg.
- n_total:
Number of total pixels at a given distance.
- n_valid:
Number of valid pixels (with non-NaN values after balancing) at a given distance.
- count.sum:
Sum up raw contact counts of all pixels at a given distance.
- count.avg:
The average raw contact count of pixels at a given distance. count.sum / n_total.
When clr_weigh_name is provided (by default, clr_weigh_name=”weight”), the following quantities (columns) will be added into the DataFrame:
- balanced.sum:
Sum up balanced contact values of valid pixels at a given distance. Returned if clr_weight_name is not None.
- balanced.avg:
The average balanced contact values of valid pixels at a given distance. balanced.sum / n_valid. Returned if clr_weight_name is not None.
When smooth=True, the following quantities (columns) will be added into the DataFrame:
- count.avg.smoothed:
Log-smoothed count.avg. Returned if smooth=True and clr_weight_name=None.
- balanced.avg.smoothed:
Log-smoothed balanced.avg. Returned if smooth=True and clr_weight_name is not None.
- When aggregate_smoothed=True, the following quantities (columns) will be added into the DataFrame:
- count.avg.smoothed.agg:
Aggregate Log-smoothed count.avg of all genome regions. Returned if smooth=True and aggregate_smoothed=True and clr_weight_name=None.
- balanced.avg.smoothed.agg:
Aggregate Log-smoothed balanced.avg of all genome regions. Returned if smooth=True and aggregate_smoothed=True and clr_weight_name is not None.
By default, clr_weight_name=”weight”, smooth=True, aggregate_smoothed=True, the output DataFrame includes all quantities (columns).
- cooltools.api.expected.expected_trans(clr, view_df=None, clr_weight_name='weight', chunksize=10000000, nproc=1, map_functor=<class 'map'>)[source]
Calculate average interaction frequencies for inter-chromosomal blocks defined as pairwise combinations of regions in view_df.
An expected level of interactions between disjoint chromosomes is calculated as a simple average, as there is no notion of genomic separation for a pair of chromosomes and contact matrix for these regions looks “flat”.
Average values are reported in the columns with names {}.avg, and they are calculated as a ratio between a corresponding sum {}.sum and the total number of “valid” pixels on the diagonal “n_valid”.
- Parameters
clr (cooler.Cooler) – Cooler object
view_df (viewframe) – a collection of genomic intervals where expected is calculated otherwise expected is calculated for full chromosomes, has to be sorted.
clr_weight_name (str or None) – Name of balancing weight column from the cooler to use. Use raw unbalanced data, when None.
chunksize (int, optional) – Size of pixel table chunks to process
nproc (int, optional) – How many processes to use for calculation. Ignored if map_functor is passed.
map_functor (callable, optional) – Map function to dispatch the matrix chunks to workers. If left unspecified, pool_decorator applies the following defaults: if nproc>1 this defaults to multiprocess.Pool; If nproc=1 this defaults the builtin map.
- Returns
DataFrame with summary statistic for every trans-blocks
region1, region2, n_valid, count.sum count.avg, etc
- cooltools.api.expected.genomewide_smooth_cvd(cvd, sigma_log10=0.1, window_sigma=5, points_per_sigma=10, cols=None, suffix='.smoothed')[source]
Smooth the contact-vs-distance curve aggregated across all regions in log-space.
- Parameters
cvd (pandas.DataFrame) – A dataframe with the expected values in the cooltools.expected format.
sigma_log10 (float, optional) – The standard deviation of the smoothing Gaussian kernel, applied over log10(diagonal), by default 0.1
window_sigma (int, optional) – Width of the smoothing window, expressed in sigmas, by default 5
points_per_sigma (int, optional) – If provided, smoothing is done only for points_per_sigma points per sigma and the rest of the values are interpolated (this results in a major speed-up). By default 10
cols (dict, optional) – If provided, use the specified column names instead of the standard ones. See DEFAULT_CVD_COLS variable for the format of this argument.
suffix (string, optional) – If provided, use the specified string as the suffix of the output column’s name
- Returns
cvd (pandas.DataFrame) – A cvd table with extra column for the log-smoothed contact frequencies (by default, “balanced.avg.smoothed.agg” if balanced, or “count.avg.smoothed.agg” if raw).
Notes
Parameters in “cols” will be used:
- dist:
Name of the column that stores distance values (by default, “dist”).
- n_pixels:
Name of the column that stores number of pixels (by default, “n_valid” if balanced, or “n_total” if raw).
- n_contacts:
Name of the column that stores the sum of contacts (by default, “balanced.sum” if balanced, or “count.sum” if raw).
- output_prefix:
Name prefix of the column that will store output value (by default, “balanced.avg” if balanced, or “count.avg” if raw).
- cooltools.api.expected.interpolate_expected(expected, binned_expected, columns=['balanced.avg'], kind='quadratic', by_region=True, extrapolate_small_s=False)[source]
Interpolates expected to match binned_expected. Basically, this function smoothes the original expected according to the logbinned expected. It could either use by-region expected (each region will have different expected) or use combined binned_expected (all regions will have the same expected after that)
Such a smoothed expected should be used to calculate observed/expected for downstream analysis.
- Parameters
expected (pd.DataFrame) – expected as returned by diagsum_symm
binned_expected (pd.DataFrame) – binned expected (combined or not)
columns (list[str] (optional)) – Columns to interpolate. Must be present in binned_expected, but not necessarily in expected.
kind (str (optional)) – Interpolation type, according to scipy.interpolate.interp1d
by_region (bool or str (optional)) – Whether to do interpolation by-region (default=True). False means use one expected for all regions (use entire table). If a region name is provided, expected for that region is used.
- cooltools.api.expected.lattice_pdist_frequencies(n, points)[source]
Distribution of pairwise 1D distances among a collection of distinct integers ranging from 0 to n-1.
- Parameters
n (int) – Size of the lattice on which the integer points reside.
points (sequence of int) – Arbitrary integers between 0 and n-1, inclusive, in any order but with no duplicates.
- Returns
h (1D array of length n) – h[d] counts the number of integer pairs that are exactly d units apart
Notes
This is done using a convolution via FFT. Thanks to Peter de Rivaz; see http://stackoverflow.com/questions/42423823/distribution-of-pairwise-distances-between-many-integers.
- cooltools.api.expected.logbin_expected(exp, summary_name='balanced.sum', bins_per_order_magnitude=10, bin_layout='fixed', smooth=<function <lambda>>, min_nvalid=200, min_count=50)[source]
Logarithmically bins expected as produced by diagsum_symm method.
- Parameters
exp (DataFrame) – DataFrame produced by diagsum_symm
summary_name (str, optional) – Name of the column of exp-DataFrame to use as a diagonal summary. Default is “balanced.sum”.
bins_per_order_magnitude (int, optional) – How many bins per order of magnitude. Default of 10 has a ratio of neighboring bins of about 1.25
bin_layout ("fixed", "longest_region", or array) –
“fixed” means that bins are exactly the same for different datasets, and only depend on bins_per_order_magnitude
”longest_region” means that the last bin will end at size of the longest region.
GOOD: the last bin will have as much data as possible. BAD: bin edges will end up different for different datasets, you can’t divide them by each other
array: provide your own bin edges. Can be of any size, and end at any value. Bins exceeding the size of the largest region will be simply ignored.
smooth (callable) – A smoothing function to be applied to log(P(s)) and log(x) before calculating P(s) slopes for by-region data
min_nvalid (int) – For each region, throw out bins (log-spaced) that have less than min_nvalid valid pixels This will ensure that each entree in Pc_by_region has at least n_valid valid pixels Don’t set it to zero, or it will introduce bugs. Setting it to 1 is OK, but not recommended.
min_count (int) – If counts are found in the data, then for each region, throw out bins (log-spaced) that have more than min_counts of counts.sum (raw Hi-C counts). This will ensure that each entree in Pc_by_region has at least min_count raw Hi-C reads
- Returns
Pc (DataFrame) – dataframe of contact probabilities and spread across regions
slope (ndarray) – slope of Pc(s) on a log-log plot and spread across regions
bins (ndarray) – an array of bin edges used for calculating P(s)
Notes
For main Pc and slope, the algorithm is the following
concatenate all the expected for all regions into a large dataframe.
create logarithmically-spaced bins of diagonals (or use provided)
pool together n_valid and balanced.sum for each region and for each bin
calculate the average diagonal for each bucket, weighted by n_valid
divide balanced.sum by n_valid after summing for each bucket (not before)
calculate the slope in log space (for each region)
X values are not midpoints of bins
In step 4, we calculate the average diag index weighted by n_valid. This seems counter-intuitive, but it actually is justified.
Let’s take the worst case scenario. Let there be a bin from 40MB to 44MB. Let there be a region that is exactly 41 MB long. The midpoint of the bin is at 42MB. But the only part of this region belonging to this bin is actually between 40MB and 41MB. Moreover, the “average” read in this little triangle of the heatmap is actually not coming even from 40.5 MB because the triangle is getting narrower towards 41MB. The center of mass of a triangle is 1/3 of the way up, or 40.33 MB. So an average read for this region in this bin is coming from 40.33.
Consider the previous bin, say, from 36MB to 40MB. The heatmap there is a trapezoid with a long side of 5MB, the short side of 1MB, and height of 4MB. The center of mass of this trapezoid is at 36 + 14/9 = 37.55MB, and not at 38MB. So the last bin center is definitely mis-assigned, and the second-to-last bin center is off by some 25%. This would lead to a 25% error of the P(s) slope estimated between the third-to-last and second-to-last bin.
In presence of missing bins, this all becomes more complex, but this kind of averaging should take care of everything. It follows a general principle: when averaging the y values with some weights, one needs to average the x values with the same weights. The y values here are being added together, so per-diag means are effectively averaged with the weight of n_valid. Therefore, the x values (diag) should be averaged with the same weights.
Other considerations
Steps #3 and #5 are important because the ratio of sums does not equal to the sum of ratios, and the former is more correct (the latter is more susceptible to noise). It is generally better to divide at the very end, rather than dividing things for each diagonal.
Here we divide at the end twice: first we divide balanced.sum by n_valid for each region, then we effectively multiply it back up and divide it for each bin when combining different regions (see weighted average in the next function).
Smoothing P(s) for the slope
For calcuating the slope, we apply smoothing to the P(s) to ensure the slope is not too noisy. There are several caveats here: the P(s) has to be smoothed in logspace, and both P and s have to be smoothed. It is discussed in detail here
https://gist.github.com/mimakaev/4becf1310ba6ee07f6b91e511c531e73
Examples
For example, see this gist: https://gist.github.com/mimakaev/e9117a7fcc318e7904702eba5b47d9e6
- cooltools.api.expected.make_block_table(clr, regions1, regions2, clr_weight_name='weight')[source]
Creates a table of total and valid pixels for a set of rectangular genomic blocks defined by regions1 and regions2. For every block calculate its “area” in pixels (“n_total”), and calculate number of “valid” pixels (“n_valid”). Valid pixels exclude “bad” pixels, which are inferred from the balancing weight column clr_weight_name.
When clr_weight_name is None, raw data is used, and no “bad” pixels are exclued.
- Parameters
clr (cooler.Cooler) – Input cooler
regions1 (viewframe-like dataframe) – viewframe-like dataframe, where repeated entries are allowed
regions2 (viewframe-like dataframe) – viewframe-like dataframe, where repeated entries are allowed
clr_weight_name (str) – name of the weight column in the cooler bins-table, used for masking bad pixels. When clr_weight_name is None, no bad pixels are masked.
- Returns
block_table (dict) – dictionary for blocks that are 0-indexed
- cooltools.api.expected.make_diag_table(bad_mask, span1, span2)[source]
Compute the total number of elements
n_totaland the number of bad elementsn_badper diagonal for a single contact area encompassingspan1andspan2on the same genomic scaffold (cis matrix).Follows the same principle as the algorithm for finding contact areas for computing scalings.
- Parameters
bad_mask (1D array of bool) – Mask of bad bins for the whole genomic scaffold containing the regions of interest.
span1 (pair of ints) – The bin spans (not genomic coordinates) of the two regions of interest.
span2 (pair of ints) – The bin spans (not genomic coordinates) of the two regions of interest.
- Returns
diags (pandas.DataFrame) – Table indexed by ‘diag’ with columns [‘n_total’, ‘n_bad’].
- cooltools.api.expected.make_diag_tables(clr, regions, regions2=None, clr_weight_name='weight')[source]
For every region infer diagonals that intersect this region and calculate the size of these intersections in pixels, both “total” and “n_valid”, where “n_valid” does not count “bad” pixels.
“Bad” pixels are inferred from the balancing weight column clr_weight_name. When clr_weight_name is None, raw data is used, and no “bad” pixels are exclued.
When regions2 are provided, all intersecting diagonals are reported for each rectangular and asymmetric block defined by combinations of matching elements of regions and regions2. Otherwise only regions-based symmetric square blocks are considered. Only intra-chromosomal regions are supported.
- Parameters
clr (cooler.Cooler) – Input cooler
regions (viewframe or viewframe-like dataframe) – viewframe without repeated entries or viewframe-like dataframe with repeated entries
regions2 (viewframe or viewframe-like dataframe) – viewframe without repeated entries or viewframe-like dataframe with repeated entries
clr_weight_name (str) – name of the weight column in the clr bin-table, Balancing weight is used to infer bad bins, set to None is masking bad bins is not desired for raw data.
- Returns
diag_tables (dict) – dictionary with DataFrames of relevant diagonals for every region.
- cooltools.api.expected.per_region_smooth_cvd(cvd, sigma_log10=0.1, window_sigma=5, points_per_sigma=10, cols=None, suffix='')[source]
Smooth the contact-vs-distance curve for each region in log-space.
- Parameters
cvd (pandas.DataFrame) – A dataframe with the expected values in the cooltools.expected format.
sigma_log10 (float, optional) – The standard deviation of the smoothing Gaussian kernel, applied over log10(diagonal), by default 0.1
window_sigma (int, optional) – Width of the smoothing window, expressed in sigmas, by default 5
points_per_sigma (int, optional) – If provided, smoothing is done only for points_per_sigma points per sigma and the rest of the values are interpolated (this results in a major speed-up). By default 10
cols (dict, optional) – If provided, use the specified column names instead of the standard ones. See DEFAULT_CVD_COLS variable for the format of this argument.
suffix (string, optional) – If provided, use the specified string as the suffix of the output column’s name
- Returns
cvd (pandas.DataFrame) – A cvd table with extra column for the log-smoothed contact frequencies (by default, “balanced.avg.smoothed” if balanced, or “count.avg.smoothed” if raw).
Notes
Parameters in “cols” will be used:
- region1:
Name of the column that stores region1’s locations (by default, “region1”).
- region2:
Name of the column that stores region2’s locations (by default, “region2”).
- dist:
Name of the column that stores distance values (by default, “dist”).
- n_pixels:
Name of the column that stores number of pixels (by default, “n_valid” if balanced, or “n_total” if raw).
- n_contacts:
Name of the column that stores the sum of contacts (by default, “balanced.sum” if balanced, or “count.sum” if raw).
- output_prefix:
Name prefix of the column that will store output value (by default, “balanced.avg” if balanced, or “count.avg” if raw).
cooltools.api.insulation module
- cooltools.api.insulation.calculate_insulation_score(clr, window_bp, view_df=None, ignore_diags=None, min_dist_bad_bin=0, is_bad_bin_key='is_bad_bin', append_raw_scores=False, chunksize=20000000, clr_weight_name='weight', verbose=False, nproc=1, map_functor=<class 'map'>)[source]
Calculate the diamond insulation scores for all bins in a cooler.
- Parameters
clr (cooler.Cooler) – A cooler with balanced Hi-C data.
window_bp (int or list of integers) – The size of the sliding diamond window used to calculate the insulation score. If a list is provided, then a insulation score if calculated for each value of window_bp.
view_df (bioframe.viewframe or None) – Viewframe for independent calculation of insulation scores for regions
ignore_diags (int | None) – The number of diagonals to ignore. If None, equals the number of diagonals ignored during IC balancing.
min_dist_bad_bin (int) – The minimal allowed distance to a bad bin to report insulation score. Fills bins that have a bad bin closer than this distance by nans.
is_bad_bin_key (str) – Name of the output column to store bad bins
append_raw_scores (bool) – If True, append columns with raw scores (sum_counts, sum_balanced, n_pixels) to the output table.
clr_weight_name (str or None) – Name of the column in the bin table with weight. Using unbalanced data with None will avoid masking “bad” pixels.
verbose (bool) – If True, report real-time progress.
nproc (int, optional) – How many processes to use for calculation. Ignored if map_functor is passed.
map_functor (callable, optional) – Map function to dispatch the matrix chunks to workers. If left unspecified, pool_decorator applies the following defaults: if nproc>1 this defaults to multiprocess.Pool; If nproc=1 this defaults the builtin map.
- Returns
ins_table (pandas.DataFrame) – A table containing the insulation scores of the genomic bins
- cooltools.api.insulation.find_boundaries(ins_table, min_frac_valid_pixels=0.66, min_dist_bad_bin=0, log2_ins_key='log2_insulation_score_{WINDOW}', n_valid_pixels_key='n_valid_pixels_{WINDOW}', is_bad_bin_key='is_bad_bin')[source]
Call insulating boundaries.
Find all local minima of the log2(insulation score) and calculate their chromosome-wide topographic prominence.
- Parameters
ins_table (pandas.DataFrame) – A bin table with columns containing log2(insulation score), annotation of regions (required), the number of valid pixels per diamond and (optionally) the mask of bad bins. Normally, this should be an output of calculate_insulation_score.
view_df (bioframe.viewframe or None) – Viewframe for independent boundary calls for regions
min_frac_valid_pixels (float) – The minimal fraction of valid pixels in a diamond to be used in boundary picking and prominence calculation.
min_dist_bad_bin (int) – The minimal allowed distance to a bad bin to be used in boundary picking. Ignore bins that have a bad bin closer than this distance.
log2_ins_key (str) – The names of the columns containing log2_insulation_score and the number of valid pixels per diamond. When a template containing {WINDOW} is provided, the calculation is repeated for all pairs of columns matching the template.
n_valid_pixels_key (str) – The names of the columns containing log2_insulation_score and the number of valid pixels per diamond. When a template containing {WINDOW} is provided, the calculation is repeated for all pairs of columns matching the template.
- Returns
ins_table (pandas.DataFrame) – A bin table with appended columns with boundary prominences.
- cooltools.api.insulation.get_n_pixels(bad_bin_mask, window=10, ignore_diags=2)[source]
Calculate the number of “good” pixels in a diamond at each bin.
- cooltools.api.insulation.insul_diamond(pixel_query, bins, window=10, ignore_diags=2, norm_by_median=True, clr_weight_name='weight')[source]
Calculates the insulation score of a Hi-C interaction matrix.
- Parameters
pixel_query (RangeQuery object <TODO:update description>) – A table of Hi-C interactions. Must follow the Cooler columnar format: bin1_id, bin2_id, count, balanced (optional)).
bins (pandas.DataFrame) – A table of bins, is used to determine the span of the matrix and the locations of bad bins.
window (int) – The width (in bins) of the diamond window to calculate the insulation score.
ignore_diags (int) – If > 0, the interactions at separations < ignore_diags are ignored when calculating the insulation score. Typically, a few first diagonals of the Hi-C map should be ignored due to contamination with Hi-C artifacts.
norm_by_median (bool) – If True, normalize the insulation score by its NaN-median.
clr_weight_name (str or None) – Name of balancing weight column from the cooler to use. Using raw unbalanced data is not supported for insulation.
- cooltools.api.insulation.insulation(clr, window_bp, view_df=None, ignore_diags=None, clr_weight_name='weight', min_frac_valid_pixels=0.66, min_dist_bad_bin=0, threshold='Li', append_raw_scores=False, chunksize=20000000, verbose=False, nproc=1)[source]
Find insulating boundaries in a contact map via the diamond insulation score.
For a given cooler, this function (a) calculates the diamond insulation score track, (b) detects all insulating boundaries, and (c) removes weak boundaries via an automated thresholding algorithm.
- Parameters
clr (cooler.Cooler) – A cooler with balanced Hi-C data.
window_bp (int or list of integers) – The size of the sliding diamond window used to calculate the insulation score. If a list is provided, then a insulation score if done for each value of window_bp.
view_df (bioframe.viewframe or None) – Viewframe for independent calculation of insulation scores for regions
ignore_diags (int | None) – The number of diagonals to ignore. If None, equals the number of diagonals ignored during IC balancing.
clr_weight_name (str) – Name of the column in the bin table with weight
min_frac_valid_pixels (float) – The minimal fraction of valid pixels in a diamond to be used in boundary picking and prominence calculation.
min_dist_bad_bin (int) – The minimal allowed distance to a bad bin to report insulation score. Fills bins that have a bad bin closer than this distance by nans.
threshold ("Li", "Otsu" or float) – Rule used to threshold the histogram of boundary strengths to exclude weak boundaries. “Li” or “Otsu” use corresponding methods from skimage.thresholding. Providing a float value will filter by a fixed threshold
append_raw_scores (bool) – If True, append columns with raw scores (sum_counts, sum_balanced, n_pixels) to the output table.
verbose (bool) – If True, report real-time progress.
nproc (int, optional) – How many processes to use for calculation
- Returns
ins_table (pandas.DataFrame) – A table containing the insulation scores of the genomic bins
cooltools.api.saddle module
- cooltools.api.saddle.digitize(track, n_bins, vrange=None, qrange=None, digitized_suffix='.d')[source]
Digitize genomic signal tracks into integers between 1 and n.
- Parameters
track (4-column DataFrame) – bedGraph-like dataframe with columns understood as (chrom,start,end,value).
n_bins (int) – number of bins for signal quantization.
vrange (tuple) – Low and high values used for binning track values. E.g. if `vrange`=(-0.05, 0.05), equal width bins would be generated between the value -0.05 and 0.05.
qrange (tuple) – Low and high values for quantile binning track values. E.g., if `qrange`=(0.02, 0.98) the lower bin would start at the 2nd percentile and the upper bin would end at the 98th percentile of the track value range. Low must be 0.0 or more, high must be 1.0 or less.
digitized_suffix (str) – suffix to append to the track value name in the fourth column.
- Returns
digitized (DataFrame) – New track dataframe (bedGraph-like) with digitized value column with name suffixed by ‘.d’ The digized column is returned as a categorical.
binedges (1D array (length n + 1)) – Bin edges used in quantization of track. For n bins, there are n + 1 edges. See encoding details in Notes.
Notes
The digital encoding is as follows:
1..n <-> values assigned to bins defined by vrange or qrange
0 <-> left outlier values
n+1 <-> right outlier values
-1 <-> missing data (NaNs)
- cooltools.api.saddle.saddle(clr, expected, track, contact_type, n_bins, vrange=None, qrange=None, view_df=None, clr_weight_name='weight', expected_value_col='balanced.avg', view_name_col='name', min_diag=3, max_diag=-1, trim_outliers=False, verbose=False, drop_track_na=False)[source]
Get a matrix of average interactions between genomic bin pairs as a function of a specified genomic track.
The provided genomic track is either: (a) digitized inside this function by passing ‘n_bins’, and one of ‘v_range’ or ‘q_range’ (b) passed as a pre-digitized track with a categorical value column as generated by get_digitized().
- Parameters
clr (cooler.Cooler) – Observed matrix.
expected (DataFrame in expected format) – Diagonal summary statistics for each chromosome, and name of the column with the values of expected to use.
contact_type (str) – If ‘cis’ then only cis interactions are used to build the matrix. If ‘trans’, only trans interactions are used.
track (DataFrame) – A track, i.e. BedGraph-like dataframe, which is digitized with the options n_bins, vrange and qrange. Can optionally be passed as a pre-digitized dataFrame with a categorical value column, as generated by get_digitzied(), also passing n_bins as None.
n_bins (int or None) – number of bins for signal quantization. If None, then track must be passed as a pre-digitized track.
vrange (tuple) – Low and high values used for binning track values. See get_digitized().
qrange (tuple) – Low and high values for quantile binning track values. Low must be 0.0 or more, high must be 1.0 or less. Only one of vrange or qrange can be passed. See get_digitzed().
view_df (viewframe) – Viewframe with genomic regions. If none, generate from track chromosomes.
clr_weight_name (str) – Name of the column in the clr.bins to use as balancing weights. Using raw unbalanced data is not supported for saddles.
expected_value_col (str) – Name of the column in expected used for normalizing.
view_name_col (str) – Name of column in view_df with region names.
min_diag (int) – Smallest diagonal to include in computation. Ignored with contact_type=trans.
max_diag (int) – Biggest diagonal to include in computation. Ignored with contact_type=trans.
trim_outliers (bool, optional) – Remove first and last row and column from the output matrix.
verbose (bool, optional) – If True then reports progress.
drop_track_na (bool, optional) – If True then drops NaNs in input track (as if they were missing), If False then counts NaNs as present in dataframe. In general, this only adds check form chromosomes that have all missing values, but does not affect the results.
- Returns
interaction_sum (2D array) – The matrix of summed interaction probability between two genomic bins given their values of the provided genomic track.
interaction_count (2D array) – The matrix of the number of genomic bin pairs that contributed to the corresponding pixel of
interaction_sum.
- cooltools.api.saddle.saddle_strength(S, C)[source]
- Parameters
S (2D arrays, square, same shape) – Saddle sums and counts, respectively
C (2D arrays, square, same shape) – Saddle sums and counts, respectively
- Returns
1D array
Ratios of cumulative corner interaction scores, where the saddle data is
grouped over the AA+BB corners and AB+BA corners with increasing extent.
- cooltools.api.saddle.saddleplot(track, saddledata, n_bins, vrange=None, qrange=(0.0, 1.0), cmap='coolwarm', scale='log', vmin=0.5, vmax=2, color=None, title=None, xlabel=None, ylabel=None, clabel=None, fig=None, fig_kws=None, heatmap_kws=None, margin_kws=None, cbar_kws=None, subplot_spec=None)[source]
Generate a saddle plot.
- Parameters
track (pd.DataFrame) – See get_digitized() for details.
saddledata (2D array-like) – Saddle matrix produced by make_saddle. It will include 2 flanking rows/columns for outlier signal values, thus the shape should be (n+2, n+2).
cmap (str or matplotlib colormap) – Colormap to use for plotting the saddle heatmap
scale (str) – Color scaling to use for plotting the saddle heatmap: log or linear
vmin (float) – Value limits for coloring the saddle heatmap
vmax (float) – Value limits for coloring the saddle heatmap
color (matplotlib color value) – Face color for margin bar plots
fig (matplotlib Figure, optional) – Specified figure to plot on. A new figure is created if none is provided.
fig_kws (dict, optional) – Passed on to plt.Figure()
heatmap_kws (dict, optional) – Passed on to ax.imshow()
margin_kws (dict, optional) – Passed on to ax.bar() and ax.barh()
cbar_kws (dict, optional) – Passed on to plt.colorbar()
subplot_spec (GridSpec object) – Specify a subregion of a figure to using a GridSpec.
- Returns
Dictionary of axes objects.
cooltools.api.sample module
- cooltools.api.sample.sample(clr, out_clr_path, count=None, cis_count=None, frac=None, exact=False, chunksize=10000000, nproc=1, map_functor=<class 'map'>)[source]
Pick a random subset of contacts from a Hi-C map.
- Parameters
clr (cooler.Cooler or str) – A Cooler or a path/URI to a Cooler with input data.
out_clr_path (str) – A path/URI to the output.
count (int) – The target number of contacts in the sample. Mutually exclusive with cis_count and frac.
cis_count (int) – The target number of cis contacts in the sample. Mutually exclusive with count and frac.
frac (float) – The target sample size as a fraction of contacts in the original dataset. Mutually exclusive with count and cis_count.
exact (bool) – If True, the resulting sample size will exactly match the target value. Exact sampling will load the whole pixel table into memory! If False, binomial sampling will be used instead and the sample size will be randomly distributed around the target value.
chunksize (int) – The number of pixels loaded and processed per step of computation.
nproc (int, optional) – How many processes to use for calculation. Ignored if map_functor is passed.
map_functor (callable, optional) – Map function to dispatch the matrix chunks to workers. If left unspecified, pool_decorator applies the following defaults: if nproc>1 this defaults to multiprocess.Pool; If nproc=1 this defaults the builtin map.
cooltools.api.snipping module
Collection of classes and functions used for snipping and creation of pileups (averaging of multiple small 2D regions) The main user-facing function of this module is pileup, it performs pileups using snippers and other functions defined in the module. The concept is the following:
First, the provided features are annotated with the regions from a view (or simply whole chromosomes, if no view is provided). They are assigned to the region that contains it, or the one with the largest overlap.
Then the features are expanded using the flank argument, and aligned to the bins of the cooler
Depending on the requested operation (whether the normalization to expected is required), the appropriate snipper object is created
A snipper can select a particular region of a genome-wide matrix, meaning it stores its sparse representation in memory. This could be whole chromosomes or chromosome arms, for example
A snipper can snip a small area of a selected region, meaning it will extract and return a dense representation of this area
For each region present, it is first `select`ed, and then all features within it are `snip`ped, creating a stack: a 3D array containing all snippets for this region
For features that are not assigned to any region, an empty snippet is returned
All per-region stacks are then combined into one, which then can be averaged to create a single pileup
The order of snippets in the stack matches the order of features, this way the stack can also be used for analysis of any subsets of original features
This procedure achieves a good tradeoff between speed and RAM. Extracting each individual snippet directly from disk would be extremely slow due to slow IO. Extracting the whole chromosomes into dense matrices is not an option due to huge memory requirements. As a warning, deeply sequenced data can still require a substantial amount of RAM at high resolution even as a sparse matrix, but typically it’s not a problem.
- class cooltools.api.snipping.CoolerSnipper(clr, cooler_opts=None, view_df=None, min_diag=2)[source]
Bases:
object- select(region1, region2)[source]
Select a portion of the cooler for snipping based on two regions in the view
In addition to returning the selected portion of the data, stores necessary information about it in the snipper object for future snipping
- Parameters
region1 (str) – Name of a region from the view
region2 (str) – Name of another region from the view.
- Returns
CSR matrix – Sparse matrix of the selected portion of the data from the cooler
- snip(matrix, region1, region2, tup)[source]
Extract a snippet from the matrix
Returns a NaN-filled array for out-of-bounds regions. Fills in NaNs based on the cooler weight, if using balanced data. Fills NaNs in all diagonals below min_diag
- Parameters
matrix (SCR matrix) – Output of the .select() method
region1 (str) – Name of a region from the view corresponding to the matrix
region2 (str) – Name of the other regions from the view corresponding to the matrix
tup (tuple) – (start1, end1, start2, end2) coordinates of the requested snippet in bp
- Returns
np.array – Requested snippet.
- class cooltools.api.snipping.ExpectedSnipper(clr, expected, view_df=None, min_diag=2, expected_value_col='balanced.avg')[source]
Bases:
object- select(region1, region2)[source]
Select a portion of the expected matrix for snipping based on two regions in the view
In addition to returning the selected portion of the data, stores necessary information about it in the snipper object for future snipping
- Parameters
region1 (str) – Name of a region from the view
region2 (str) – Name of another region from the view.
- Returns
CSR matrix – Sparse matrix of the selected portion of the data from the cooler
- snip(exp, region1, region2, tup)[source]
Extract an expected snippet
Returns a NaN-filled array for out-of-bounds regions. Fills NaNs in all diagonals below min_diag
- Parameters
exp (SCR matrix) – Output of the .select() method
region1 (str) – Name of a region from the view corresponding to the matrix
region2 (str) – Name of the other regions from the view corresponding to the matrix
tup (tuple) – (start1, end1, start2, end2) coordinates of the requested snippet in bp
- Returns
np.array – Requested snippet.
- class cooltools.api.snipping.ObsExpSnipper(clr, expected, cooler_opts=None, view_df=None, min_diag=2, expected_value_col='balanced.avg')[source]
Bases:
object- select(region1, region2)[source]
Select a portion of the cooler for snipping based on two regions in the view
In addition to returning the selected portion of the data, stores necessary information about it in the snipper object for future snipping
- Parameters
region1 (str) – Name of a region from the view
region2 (str) – Name of another region from the view.
- Returns
CSR matrix – Sparse matrix of the selected portion of the data from the cooler
- snip(matrix, region1, region2, tup)[source]
Extract an expected-normalised snippet from the matrix
Returns a NaN-filled array for out-of-bounds regions. Fills in NaNs based on the cooler weight, if using balanced data. Fills NaNs in all diagonals below min_diag
- Parameters
matrix (SCR matrix) – Output of the .select() method
region1 (str) – Name of a region from the view corresponding to the matrix
region2 (str) – Name of the other regions from the view corresponding to the matrix
tup (tuple) – (start1, end1, start2, end2) coordinates of the requested snippet in bp
- Returns
np.array – Requested snippet.
- cooltools.api.snipping.expand_align_features(features_df, flank, resolution, format='bed')[source]
Short summary.
- Parameters
features_df (pd.DataFrame) – Dataframe with feature coordinates.
flank (int) – Flank size to add to the central bin of each feature.
resolution (int) – Size of the bins to use.
format (str) – “bed” or “bedpe” format: has to have ‘chrom’, ‘start’, ‘end’ or ‘chrom1’, ‘start1’, ‘end1’, ‘chrom2’, ‘start2’, ‘end1’ columns, repectively.
- Returns
pd.DataFrame –
- DataFrame with features with new columns
”center”, “orig_start” “orig_end”
- or “center1”, “orig_start1”, “orig_end1”,
”center2”, “orig_start2”, “orig_rank_end2”, depending on format.
- cooltools.api.snipping.make_bin_aligned_windows(binsize, chroms, centers_bp, flank_bp=0, region_start_bp=0, ignore_index=False)[source]
Convert genomic loci into bin spans on a fixed bin-segmentation of a genomic region. Window limits are adjusted to align with bin edges.
- Parameters
binsize (int) – Bin size (resolution) in base pairs.
chroms (1D array-like) – Column of chromosome names.
centers_bp (1D or nx2 array-like) – If 1D, center points of each window. If 2D, the starts and ends.
flank_bp (int) – Distance in base pairs to extend windows on either side.
region_start_bp (int, optional) – If region is a subset of a chromosome, shift coordinates by this amount. Default is 0.
- Returns
DataFrame with columns – ‘chrom’ - chromosome ‘start’, ‘end’ - window limits in base pairs ‘lo’, ‘hi’ - window limits in bins
- cooltools.api.snipping.pileup(clr, features_df, view_df=None, expected_df=None, expected_value_col='balanced.avg', flank=100000, min_diag='auto', clr_weight_name='weight', nproc=1, map_functor=<class 'map'>)[source]
Pileup features over the cooler.
- Parameters
clr (cooler.Cooler) – Cooler with Hi-C data
features_df (pd.DataFrame) – Dataframe in bed or bedpe format: has to have ‘chrom’, ‘start’, ‘end’ or ‘chrom1’, ‘start1’, ‘end1’, ‘chrom2’, ‘start2’, ‘end2’ columns.
view_df (pd.DataFrame) – Dataframe with the genomic view for this operation (has to match the expected_df, if provided)
expected_df (pd.DataFrame) – Dataframe with the expected level of interactions at different genomic separations
expected_value_col (str) – Name of the column in expected used for normalizing.
flank (int) – How much to flank the center of the features by, in bp
min_diag (str or int) – All diagonals of the matrix below this value are ignored. ‘auto’ tries to extract the value used during the matrix balancing, if it fails defaults to 2
clr_weight_name (str) – Value of the column that contains the balancing weights
force (bool) – Allows start>end in the features (not implemented)
nproc (int, optional) – How many processes to use for calculation. Ignored if map_functor is passed.
map_functor (callable, optional) – Map function to dispatch the matrix chunks to workers. If left unspecified, pool_decorator applies the following defaults: if nproc>1 this defaults to multiprocess.Pool; If nproc=1 this defaults the builtin map.
- Returns
np.ndarray (a stackup of all snippets corresponding to the features, with shape)
(n, D, D), where n is the number of snippets and (D, D) is the shape of each
snippet
cooltools.api.virtual4c module
- cooltools.api.virtual4c.virtual4c(clr, viewpoint, clr_weight_name='weight', nproc=1, map_functor=<class 'map'>)[source]
Generate genome-wide contact profile for a given viewpoint.
Extract all contacts of a given viewpoint from a cooler file.
- Parameters
clr (cooler.Cooler) – A cooler with balanced Hi-C data.
viewpoint (tuple or str) – Coordinates of the viewpoint.
clr_weight_name (str) – Name of the column in the bin table with weight
nproc (int, optional) – How many processes to use for calculation. Ignored if map_functor is passed.
map_functor (callable, optional) – Map function to dispatch the matrix chunks to workers. If left unspecified, pool_decorator applies the following defaults: if nproc>1 this defaults to multiprocess.Pool; If nproc=1 this defaults the builtin map.
- Returns
v4C_table (pandas.DataFrame) – A table containing the interaction frequency of the viewpoint with the rest of the genome
Note
Note: this is a new (experimental) function, the interface or output might change in a future version.
Release notes
v0.7.0
New features
Add pool decorator to functions for supporting multiprocess
expected_cisnow accepts unbalanced cool file too
API changes
expected_cisoutput cvd table now also includes “dist_bp”, “contact_frequency”, and “n_valid” columns
now returns “count.avg.smoothed” and “count.avg.smoothed.agg”, when
clr_weight_name=None, smooth=True, aggregate_smoothed=True
Maintenance
Replaced np.int with int in adaptive_coarsegrain
OE update in sandbox
Cross score sandbox fixes
Support for pandas 2
v0.6.0
New features
New function/tool
rearrange_coolerto reorder/subset/flip regions of the genome in a coolerNew test dataset for micro-C from hESCs
API changes
snipping: reorder the axes of the output snipper array to (snippet_idx, i, j).
Maintenance
snipping: fix spurious nan->0 conversion of bad bins in on-diagonal pileups
snipping: fix snipping without provided view
snipping: fix for storing the stack in a file
virtual4c: fix for the case when viewpoint has no contacts
fix: Fix numba deprecation warnings by adding
nopython=TrueOther small bugfixes
v0.5.3
Maintenance
Improvements for
read_expected_from_fileBug fix for dot caller 0/0 occurrences
Remove
cytoolzdependencyPin cooler <0.9 until compatibility
v0.5.2
API changes
remove custom bad_bins from expected & eigdecomp #336
coverage can store total cis counts in the cooler, and sampling can use cis counts #332
can now calculate coverge for balanced data #385
new drop_track_na argument for align_track_with_cooler, allows calcultions that that missing data in tracks as absent #360
multi-thread insulation by chromosome (TODO: by chunk)
Virtual 4C tool #378
CLI changes
CLI tool for
coverage()
Documentation
snipping documentation
dots tutorial
CLI tutorial
Maintenance
Dropped support for Python 3.7 (due to Pandas compatability issues)
Added support for Python 3.10
Minor bugfixes and compatibility updates
Pandas compatibility, pinned above 1.5.1
bioframe compatability
scikit-learn, pinned above >=1.1.2
saddle binedges, value limits #361
pileup CLI bugfix for reading features
Other
v0.5.1
API changes
cooltools.dots is the new user-facing function for calling dots
Maintenance
Compatibility with pandas 1.4
Strict dictinary typing for new numba versions
Update to bioframe 0.3.3
v0.5.0
NOTE: THIS RELEASE BREAKS BACKWARDS COMPATIBILITY!
This release addresses two major issues:
Integration with bioframe viewframes defined as of bioframe v0.3.
Synchronization of the CLI and Python API
Additionally, the documentation has been greatly improved and now includes detailed tutorials that show how to use the cooltools API in conjunction with other Open2C libraries. These tutorials are automatically re-built from notebooks copied from https://github.com/open2c/open2c_examples repository.
API changes
More clear separation of top-level user-facing functions and low-level API.
Most standard analyses can be performed using just the user-facing functions which are imported into the top-level namespace. Some of them are new or heavily modified from earlier versions.
cooltools.expected_cisandcooltools.expected_transfor average by-diagonal contact frequency in intra-chromosomal data and in inter-chromosomal data, respectivelycooltools.eigs_cisandcooltools.eigs_transfor eigenvectors (compartment profiles) of cis and trans data, repectivelycooltools.digitizeandcooltools.saddlecan be used together for creation of 2D summary tables of Hi-C interactions in relation to a digitized genomic track, such as eigenvectorscooltools.insulationfor insulation score and annotation of insulating boundariescooltools.directionalityfor directionality indexcooltools.pileupfor average signal at 1D or 2D genomic features, including APAcooltools.coveragefor calculation of per-bin sequencing depthcooltools.samplefor random downsampling of cooler filesFor non-standard analyses that require custom algorithms, a lower level API is available under
cooltools.api
Most functions now take an optional
view_dfargument. A pandas dataframe defining a genomic view (https://bioframe.readthedocs.io/en/latest/guide-technical-notes.html) can be provided to limit the analyses to regions included in the view. If not provided, the analysis is performed on whole chromosomes according to what’s stored in the cooler.All functions apart from
coveragenow take aclr_weight_nameargument to specify how the desired balancing weight column is named. Providing aNonevalue allows one to use unbalanced data (except theeigs_cis,eigs_transmethods, since eigendecomposition is only defined for balanced Hi-C data).The output of
expected-cisfunction has changed: it now containsregion1andregion2columns (with identical values in case of within-region expected). Additionally, it now allows smoothing of the result to avoid noisy values at long distances (enabled by default and result saved in additional columns of the dataframe)The new
cooltools.insulationmethod includes a thresholding step to detect strong boundaries, using either the Li or the Otsu method (fromskimage.thresholding), or a fixed float value. The result of thresholding for each window size is stored as a boolean in a new columnis_boundary_{window}.New subpackage
sandboxfor experimental codes that are either candidates for merging into cooltools or candidates for removal. No documentation and tests are expected, proceed at your own risk.New subpackage
libfor auxiliary modules
CLI changes
CLI tools are renamed with prefixes dropped (e.g.
diamond-insulationis nowinsulation), to align with names of user-facing API functions.The CLI tool for expected has been split in two for intra- and inter-chromosomal data (
expected-cisandexpected-trans, repectively).Similarly, the compartment profile calculation is now separate for cis and trans (
eigs-cisandeigs-trans).New CLI tool
cooltools pileupfor creation of average features based on Hi-C data. It takes a .bed- or .bedpe-style file to create average on-diagonal or off-diagonal pileups, respectively.
Maintenance
Support for Python 3.6 dropped
v0.4.0
Date: 2021-04-06
Maintenance
Make saddle strength work with NaNs
Add output option to diamond-insulation
Upgrade bioframe dependency
Parallelize random sampling
Various compatibility fixes to expected, saddle and snipping and elsewhere to work with standard formats for “expected” and “regions”: https://github.com/open2c/cooltools/issues/217
New features
New dataset download API
New functionality for smoothing P(s) and derivatives (API is not yet stable):
logbin_expected,interpolate_expected
v0.3.2
Date: 2020-05-05
Updates and bug fixes
Error checking for vmin/vmax in compute-saddle
Various updates and fixes to expected and dot-caller code
Project health
Added docs on RTD, tutorial notebooks, code formatting, linting, and contribution guidelines.
v0.3.0
Date: 2019-11-04
Several library utilities added:
plotting.gridspec_inches,adaptive_coarsegrain, singleton interpolation, and colormaps.New tools:
cooltools samplefor random downsampling,cooltools coveragefor marginalization.
Improvements to saddle functions:
compute-saddlenow saves saddledata without transformation, and thescaleargument (with optionslogorlinear) now only determines how the saddle is plotted. Consequently,saddleplotfunction now expects untransformedsaddledata, and plots it directly or with log-scaling of the colormap. (https://github.com/open2c/cooltools/pull/105)Added
saddle.mask_bad_binsmethod to filter bins in a track based on Hi-C bin-level filtering - improves saddle and histograms when using ChIP-seq and similar tracks. It is automatically applied in the CLI interface. Shouldn’t affect the results when using eigenvectors calculated from the same data.make_saddlePython function andcompute-saddleCLI now allow setting min and max distance to use for calculating saddles.