shiba2sashimi 0.1.2

A utility for creating sashimi plot from Shiba output

🐕 shiba2sashimi 🍣 (v0.1.2)

A utility to create Sashimi plots, a publication-quality visualization of RNA-seq data, from Shiba output. Greatly inspired by rmats2sashimiplot and MISO's original implementation.

Quick start

shiba2sashimi -e /path/to/Shiba/experiment_table.tsv \
-s /path/to/Shiba/output/ -o img/sashimi_example.png \
--id "SE@chr2@157561213-157561293@157560260-157561542"

How to install

pip

pip install shiba2sashimi

or

git clone https://github.com/Sika-Zheng-Lab/shiba2sashimi.git
cd shiba2sashimi
pip install .

conda

conda create -n shiba2sashimi python=3.9
conda activate shiba2sashimi
conda install -c bioconda shiba2sashimi

Docker

docker pull naotokubota/shiba2sashimi

Dependencies

• python (>=3.9)
• numpy (>=1.18.0,<2.0.0)
• matplotlib (>=3.1.0)
• pysam (>=0.22.0)

Usage

usage: shiba2sashimi [-h] -e EXPERIMENT -s SHIBA -o OUTPUT [--id ID] [-c COORDINATE] [--samples SAMPLES] [--groups GROUPS] [--colors COLORS] [--extend_up EXTEND_UP] [--extend_down EXTEND_DOWN]
                     [--smoothing_window_size SMOOTHING_WINDOW_SIZE] [--font_family FONT_FAMILY] [--dpi DPI] [-v]

shiba2sashimi v0.1.2 - Create Sashimi plot from Shiba output

optional arguments:
  -h, --help            show this help message and exit
  -e EXPERIMENT, --experiment EXPERIMENT
                        Experiment table used for Shiba
  -s SHIBA, --shiba SHIBA
                        Shiba output directory
  -o OUTPUT, --output OUTPUT
                        Output file
  --id ID               Positional ID (pos_id) of the event to plot
  -c COORDINATE, --coordinate COORDINATE
                        Coordinates of the region to plot
  --samples SAMPLES     Samples to plot. e.g. sample1,sample2,sample3 Default: all samples in the experiment table
  --groups GROUPS       Groups to plot. e.g. group1,group2,group3 Default: all groups in the experiment table. Overrides --samples
  --colors COLORS       Colors for each group. e.g. red,orange,blue
  --extend_up EXTEND_UP
                        Extend the plot upstream. Only used when not providing coordinates. Default: 500
  --extend_down EXTEND_DOWN
                        Extend the plot downstream. Only used when not providing coordinates. Default: 500
  --smoothing_window_size SMOOTHING_WINDOW_SIZE
                        Window size for median filter to smooth coverage plot. Greater value gives smoother plot. Default: 21
  --font_family FONT_FAMILY
                        Font family for labels
  --dpi DPI             DPI of the output figure. Default: 300
  -v, --verbose         Increase verbosity

Authors

• Naoto Kubota (0000-0003-0612-2300)
• Liang Chen (0000-0001-6164-4553)
• Sika Zheng (0000-0002-0573-4981)