Chromograph

What is Chromograph?

Chromograph is a python package to create PNG images from genetics data such as BED and WIG files. It is primarily built to integrate with software from Clinical Genomics, UPD Tool and rhocall, but is stand-alone.

Chromograph viewing is integrated a js module in Scout Chromograph can be used to visualise chromosomes in Scout (Screenshot from Scout with Chromograph):

Usage, command line

Chromograph as used from the command line.

usage: chromograph [-h] [-a FILE] [-c FILE] [-f FILE] [-i FILE] [-m FILE]
                   [-r FILE] [-s FILE] [--step STEP] [--version] [-d FILE]
                   [-e] [-k FILE] [-n] [-u CHUNK] [-x] [--small] [--medium]
                   [--large]

optional arguments:
  -h, --help            show this help message and exit
  -a FILE, --autozyg FILE
                        Plot regions of autozygosity from bed file [OPERATION]
  -c FILE, --coverage FILE
                        Plot coverage from fixed step wig file [OPERATION]
  -f FILE, --fracsnp FILE
                        Plot fraction of homozygous SNPs from wig file
                        [OPERATION]
  -i FILE, --ideogram FILE
                        Plot ideograms from bed-file on format ['chrom',
                        'start', 'end', 'name', 'gStain'] [OPERATION]
  -m FILE, --exom FILE  Plot exom coverage from bed file [OPERATION]
  -r FILE, --regions FILE
                        Plot UPD regions from bed file [OPERATION]
  -s FILE, --sites FILE
                        Plot UPD sites from bed file [OPERATION]
  --step STEP           fixed step size (default 5000)
  --version             Display program version (1.3.0) and exit.
  -d FILE, --outd FILE  output dir
  -e, --euploid         Always output an euploid amount of files -even if some
                        are empty
  -k FILE, --rgb FILE   Set color (RGB hex, only with --coverage option)
  -n, --norm            Normalize data (wig/coverage)
  -u CHUNK, --chunk CHUNK
                        Set Matplotlib.agg.path.chunksize (default 10000)
  -x, --combine         Write all graphs to one file (default one plot per
                        file)
  --small
  --medium
  --large

One OPERATION Command is needed for Chromograph to produce output

Example

$ ./chromograph.py --autozyg rhocall.bed --outd tmp/

Usage, lib

Chromograph used as module. File must be provided, other arguments are optional. Example:

>>> import chromograph as chrm
>>> chrm.plot_ideogram("path_file.bed", 'combine', outdir=<path_output>)
>>> chrm.plot_upd(<file>, outd=<path>)
>>> chrm.plot_roh(<file>, 'combine', 'normalize', outd=<path>, step=<int>)
>>> chrm.plot_ideogram(file, 'combine', outd=<path>)
>>> chr.plot_ideogram("~/Work/files_test/cytoband.bed", 'combine', outd="/Users/Mikael/Downloads")

Data Formats

UPD WIG, Regions

UPD BED, Sites

UPD bed files are supported on format:

'chrom', 'start', 'end', 'updType'

UPD bed files are generated with the tool UPDtool. An example call: TODO

Ideogram BED

Ideogram bed files are supported on format:

IDEOGRAM_FORMAT = ['chrom', 'start', 'end', 'name', 'gStain']

Coverage WIG

ROH wig files are supported on format:

['chrom', 'coverage', 'pos']

These can be created using Tiddit. For example: TODO

Regions of Autozygosity, BED

Requirements

Chromograph runs in Python 3.

Package requirements:

• MatPlotLib
• Numpy
• Pandas
• Pyaml

Installation

pip install -r requirements.txt -e .

Deprecated Functionality

• Configuration file removed in version 0.3.2.