rmats2sashimiplot

About

This is a fork of the rmats2sashimiplot repository by the Xing lab. It contains a quick fix for producing plots with unlimited amounts of samples and colours.

--- Still under development! If you want to contribute, please feel free to do so! ---

Table of contents

• Dependencies
• Install
• Usage
• Output
• Contacts and bug reports
• Copyright and License Information

Dependencies

• Python 2.7 (Python 3 can be used after running 2to3.sh)
  • numpy
  • scipy
  • matplotlib
  • pysam
• Samtools
• bedtools

I recommend setting up a conda environment with the respective dependencies. This can be easily done using the provided environment file conda.yaml:

conda env create -f conda.yaml

Or for mamba users:

mamba env create -f conda.yaml

Install

After cloning the repo, rmats2sasmimiplot can be run without installing:

python ./src/rmats2sashimiplot/rmats2sashimiplot.py

I recommend running rmats2sashimiplot without installing.

rmats2sashimiplot can be installed with:

python ./setup.py install

If installed, rmats2sashimiplot can be run with just:

rmats2sashimiplot

Usage

BAM files must be sorted before visualization/indexing.

Examples

BAM files with coordinate and annotation

The fix lets you specify multiple input samples with colors for each tracks:

• --b1 takes input bam files as a comma-separated list
• --l1 takes track labels as comma-separated list (lengths of b1 and l1 must match)
• --color takes comma-separated list of colors in hex code, one color per track
• -c takes the genome region coordinates and a GFF3 annotation file (format see below)
• --exon_s and --intron_s take scale factors on how much to scale down exons/introns respectively.

cols=#ff8d17,#e77600,#b95e00,#8b4600
bams=./bams/sample1.bam,./bams/sample2.bam,./bams/sample3.bam,./bams/sample4.bam
labels=sample1,sample2,sample3,sample4
outdir=/path/to/outdir/
mkdir -p $outdir

python ./src/rmats2sashimiplot/rmats2sashimiplot.py \
    --b1 $bams \
    -c {chromosome}:{strand}:{start}:{end}:{/path/to/gff3} \
    --l1 $labels \
    --color $cols \
    --exon_s 1 \
    --intron_s 5 \
    --fig-height 12 \
    -o $outdir

Output

All output is written to the directory specified by -o. Under that directory:

• Sashimi_index/: contains intermediate files used to create the plot
• Sashimi_index_{Gene}_{event_id}/: like Sashimi_index/ but one directory for each rMATS event plotted
• Sashimi_plot/: contains the generated sashimi plots in .pdf format

Contacts and bug reports

If you encounter a bug using this modified version, feel free to open an issue and I will respond as soon as I can.

Copyright and License Information

See here.