Plot genome track data
Project description
gtracks
plot genome track data (for example from bigWig files)
Installation
pip3 install gtracks
or
pip3 install --user gtracks
Usage
usage: gtracks [-h] [--genes <genes.bed.gz>]
[--color-palette <#color> [<#color> ...]] [--max <float>]
[--tmp-dir <temp/file/dir>] [--width <int>]
[--genes-height <int>] [--gene-rows <int>]
<{chr:start-end,GENE}> [<track.bw> [<track.bw> ...]]
<path/to/output.{pdf,png,svg}
Plot bigWig signal tracks and gene annotations in a genomic region
positional arguments:
<{chr:start-end,GENE}>
coordinates or gene name to plot
<track.bw> bigWig files containing tracks
<path/to/output.{pdf,png,svg}>
path to output file
optional arguments:
-h, --help show this help message and exit
--genes <genes.bed.gz>
compressed 6-column BED file or 12-column BED12 file
containing gene annotations
--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
--genes-height <int> height of genes track
--gene-rows <int> number of gene rows
Examples
gtracks chr21:33031597-33041570 track1.bw track2.bw output.pdf
gtracks SOD1 track1.bw track2.bw output.png
export GTRACKS_TRACKS=track1.bw,track2.bw
gtracks SOD1 output.svg
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