shiba2sashimi 0.1.7
A utility for creating sashimi plot from Shiba output
License: MIT
Requires Python: >=3.9

# 🐕 shiba2sashimi 🍣 (v0.1.7)

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A utility to create Sashimi plots, a publication-quality visualization of RNA-seq data, from [Shiba](https://github.com/Sika-Zheng-Lab/Shiba) output. Greatly inspired by [rmats2sashimiplot](https://github.com/Xinglab/rmats2sashimiplot) and [MISO](https://miso.readthedocs.io/en/fastmiso/sashimi.html)'s original implementation.

## Quick start

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

![Sashimi plot example](https://raw.githubusercontent.com/Sika-Zheng-Lab/shiba2sashimi/main/img/sashimi_example.png)

## How to install

### pip

```bash
pip install shiba2sashimi
```

or

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

### conda

```bash
conda create -n shiba2sashimi -c bioconda -c conda-forge shiba2sashimi
conda activate shiba2sashimi
```

### Docker

```bash
docker pull naotokubota/shiba2sashimi
```

## Dependencies

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

## Usage

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

shiba2sashimi v0.1.7 - 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 working 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
  --width WIDTH         Width of the output figure. Default: 8
  --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
  --nolabel             Do not add sample labels and PSI values to the plot
  --nojunc              Do not plot junction arcs and junction read counts to the plot
  --minimum_junc_reads MINIMUM_JUNC_READS
                        Minimum number of reads to plot a junction arc. Default: 1
  --dpi DPI             DPI of the output figure. Default: 300
  -v, --verbose         Increase verbosity
```

## Contributing

Thank you for wanting to improve shiba2sashimi! If you have any bugs or questions, feel free to [open an issue](https://github.com/Sika-Zheng-Lab/shiba2sashimi/issues) or pull request.

## Citation

If you use shiba2sashimi in your research, please cite the original Shiba paper:

Kubota N, Chen L, Zheng S. [Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms](https://academic.oup.com/nar/article/53/4/gkaf098/8042001). *Nucleic Acids Research*  53(4), 2025, gkaf098.

## Authors

- Naoto Kubota ([0000-0003-0612-2300](https://orcid.org/0000-0003-0612-2300))
- Liang Chen ([0000-0001-6164-4553](https://orcid.org/0000-0001-6164-4553))
- Sika Zheng ([0000-0002-0573-4981](https://orcid.org/0000-0002-0573-4981))