gtracks

gtracks

Plot genome track data from bigWig and bedGraph files. Powered by pyGenomeTracks.

Installation

pip install gtracks

or

pip install --user gtracks

In conda

conda create -n gtracks -c conda-forge -c bioconda deeptools seaborn pybedtools gff2bed
conda activate gtracks
mamba install -c conda-forge -c bioconda pygenometracks
pip install gtracks

Examples

An example bigwig file with ATAC-seq data from the insulin region is included. You can generate a test plot like this:

gtracks INS-IGF2 test.png

You can plot your own tracks over other genomic regions by providing more positional arguments: a region or gene name and paths to one or more bigWig files. The file type of the plot will be determined by the output file extension.

gtracks chr11:2150341-2182439 track1.bw track2.bw output.pdf
gtracks INS track1.bw track2.bw output.svg

Modifying the gene annotations track

GRCh37/hg19 gene annotations are used by default, but you can plot GRCh38/hg38 genes by adding --genes GRCh38 or --genes hg38. You can use your own gene annotations file (BED or BED12 format) by providing --genes <path/to/genes.bed.gz>.

You may want to add more rows to the genes track. You can do this using the --genes-height and --gene-rows options.

gtracks INS test-genes.png --genes-height 6 --gene-rows 6

Coordinate parsing

By default, gtracks parses input coordinates according to the following regular expression:

([Cc]hr)?[0-9XYZWM]+:[0-9]+-[0-9]+$

Inputs not matching this expression are interpreted as gene names. This can cause errors if e.g. your contig names do not match the format. To change how coordinates are parsed, you can supply an alternative regular expression using the --coord-regex option. For example, the following expression allows arbitrary contig names:

--coord-regex '[\s\S]+:[0-9]+-[0-9]+$'

Changing the color palette

You can change the color palette for bigWig tracks using the --color-palette option.

gtracks INS track1.bw track2.bw track3.bw output.pdf --color-palette "#color1" "#color2" "#color3"

Setting y-axis height

By default, tracks have different y-axis heights depending on signal height. You can set a uniform y-axis height for all tracks using the --max option.

gtracks INS track1.bw track2.bw track3.bw output.pdf --max 400

For more command-line options, see the usage page below.

Example with non-human data and BED track

This example command uses data from S. polyrhiza and includes a BED track.

gtracks --genes Sp9512 7:6975000-6989000 sp9512_frond_example.bw sp9512_turion_example.bw sp9512_frond_turion_dmr.bed test-non-human.png

Environment variables

If you want to use your own bigWig files but don't want to write out their paths every time you run gtracks, you can set your own default tracks using the environment variable GTRACKS_TRACKS.

export GTRACKS_TRACKS=track1.bw,track2.bw,track3.bw
gtracks output.pdf

You can also change the default gene annotations file and color palette using environment variables GTRACKS_GENES_PATH and GTRACKS_COLOR_PALETTE.

export GTRACKS_GENES_PATH=path/to/genes.bed.gz
export GTRACKS_COLOR_PALETTE="#color1,#color2,#color3"
gtracks output.pdf

Should your genomic coordinates take a different form from the included default regex, you may set a different default regex using GTRACKS_COORD_REGEX:

export GTRACKS_COORD_REGEX='[\s\S]+:[0-9]+-[0-9]+$'

Usage

usage: gtracks [-h] [--genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38,Sp9512}>]
               [--color-palette <#color> [<#color> ...]] [--max <float>] [--tmp-dir <temp/file/dir>] [--width <int>]
               [--genes-height <int>] [--gene-rows <int>] [--x-axis {top,bottom,none}]
               [--vlines-bed <path/to/vlines.bed>] [--bed-labels]
               <{chr:start-end,GENE}> [<track.{bw,bed}> [<track.{bw,bed}> ...]] <path/to/output.{pdf,png,svg}>

Plot bigWig, bedGraph, and BED signal tracks with gene annotations in a genomic region

positional arguments:
  <{chr:start-end,GENE}>
                        coordinates or gene name to plot
  <track.{bw,bdg,bed}>      bigWig, bedGraph, or bed files containing tracks
  <path/to/output.{pdf,png,svg}>
                        path to output file

optional arguments:
  -h, --help            show this help message and exit
  --genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38,Sp9512}>
                        compressed 6-column BED file or 12-column BED12 file containing gene annotations. Alternatively,
                        providing a genome identifier will use one of the included gene tracks. (default: GRCh37)
  --flank <int>         add flanks to the plotting region
  --color-palette <#color> [<#color> ...]
                        color pallete for tracks
  --max <float>         max value of y-axis
  --tmp-dir <temp/file/dir>
                        directory for temporary files
  --width <int>         width of plot in cm (default: 40)
  --genes-height <int>  height of genes track (default: 2)
  --gene-rows <int>     number of gene rows (default: 1)
  --x-axis {top,bottom,none}
                        where to draw the x-axis (default: top)
  --vlines-bed <path/to/vlines.bed>
                        BED file defining vertical lines
  --bed-labels          include labels on BED tracks
  --coord-regex <regex>
                        regular expression indicating the format for coordinates (default: ([Cc]hr)?[0-9XY]+:[0-9]+-[0-9]+$)