paplot

Welcome to Post Analysis PLOT (paplot).

paplot creates interactive graphs from text data of genome analysis.

Read our preprint on bioRxiv.

1. Demo

Output example by paplot.

http://genomon-project.github.io/paplot/

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2. Documentation

English:

http://paplot-doc.readthedocs.org/en/latest/

Japanese:

http://paplot-doc.readthedocs.org/ja/latest/

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3. Dependency

• python >= 2.7

Required web browser for viewing result file. (Tested in the following)

• Firefox 48
• Google Chrome 44
• Internet Explorer 11

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4. Install

``` git clone https://github.com/Genomon-Project/paplot.git cd paplot

python setup.py build install --user ```

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5. Run

For example, (using sample data)

``` cd {paplot install directory}

# QC Report paplot qc example/qc_brush/data.csv ./tmp demo

# Chromosomal Aberration Report paplot ca example/ca_option/data.csv ./tmp demo

# Mutation Matrix Report paplot mutation example/mutation_option/data.csv ./tmp demo

# Mutational Signature Report paplot signature "example/signature_stack/data*.json" ./tmp demo

# pmsignature Report (see https://github.com/friend1ws/pmsignature) paplot pmsignature "example/pmsignature_stack/data*.json" ./tmp demo ```

6. Description

``` $ paplot -h usage: paplot [-h] [--version] {conf,index,qc,ca,mutation,signature,pmsignature} ...

positional arguments: {conf,index,qc,ca,mutation,signature,pmsignature} conf view config file index re-create index file qc plot QC Report ca plot Chromosomal Aberration Report mutation plot Mutation Matrix Report signature plot Mutational Signature Report pmsignature plot pmsignature Report

optional arguments: -h, --help show this help message and exit --version show program's version number and exit

```

6.1 QC Report

``` $ paplot qc -h usage: paplot qc [-h] [--configfile CONFIGFILE] [--title TITLE] [--ellipsis ELLIPSIS] [--overview OVERVIEW] [--remarks REMARKS] input outputdir projectname

positional arguments: input input files path outputdir output file path projectname project name

optional arguments: -h, --help show this help message and exit --configfile CONFIGFILE config file --title TITLE report's title --ellipsis ELLIPSIS report file's ID --overview OVERVIEW overview about report file --remarks REMARKS optional text ```

6.2 Chromosomal Aberration Report

``` $ paplot ca -h usage: paplot ca [-h] [--configfile CONFIGFILE] [--title TITLE] [--ellipsis ELLIPSIS] [--overview OVERVIEW] [--remarks REMARKS] input outputdir projectname

positional arguments: input input files path outputdir output file path projectname project name

optional arguments: -h, --help show this help message and exit --configfile CONFIGFILE config file --title TITLE report's title --ellipsis ELLIPSIS report file's ID --overview OVERVIEW overview about report file --remarks REMARKS optional text ```

6.3 Mutation Matrix Report

``` $ paplot mutation -h usage: paplot mutation [-h] [--configfile CONFIGFILE] [--title TITLE] [--ellipsis ELLIPSIS] [--overview OVERVIEW] [--remarks REMARKS] input outputdir projectname

positional arguments: input input files path outputdir output file path projectname project name

optional arguments: -h, --help show this help message and exit --configfile CONFIGFILE config file --title TITLE report's title --ellipsis ELLIPSIS report file's ID --overview OVERVIEW overview about report file --remarks REMARKS optional text ```

6.4 Mutational Signature Report

``` $ paplot signature -h usage: paplot signature [-h] [--configfile CONFIGFILE] [--title TITLE] [--ellipsis ELLIPSIS] [--overview OVERVIEW] [--remarks REMARKS] input outputdir projectname

positional arguments: input input files path outputdir output file path projectname project name

optional arguments: -h, --help show this help message and exit --configfile CONFIGFILE config file --title TITLE report's title --ellipsis ELLIPSIS report file's ID --overview OVERVIEW overview about report file --remarks REMARKS optional text ```

6.5 pmsignature Report

About pmsignaute?, see https://github.com/friend1ws/pmsignature)

``` $ paplot pmsignature -h usage: paplot pmsignature [-h] [--configfile CONFIGFILE] [--title TITLE] [--ellipsis ELLIPSIS] [--overview OVERVIEW] [--remarks REMARKS] input outputdir projectname

positional arguments: input input files path outputdir output file path projectname project name

optional arguments: -h, --help show this help message and exit --configfile CONFIGFILE config file --title TITLE report's title --ellipsis ELLIPSIS report file's ID --overview OVERVIEW overview about report file --remarks REMARKS optional text ```

7. Tree of output directory

{output_dir}
  │
  ├── {project_name}
  │     └── (Data files and html files)
  │
  ├── js
  │     └── (Javascript files)
  │
  ├── layout
  │     └── (Stylesheet and image files)
  │
  ├── lib
  │     └── (Javascript libraries of 3rd-party)
  │
  ├── style
  │     └ (Appearance configuration file)
  │
  └── index.html        <--------- Open your browser

8. License

See document LICENSE.

A. Javascript Libraries

Javascript Libraries used in paplot are listed below.

• D3.js https://d3js.org/
• d3-legend http://d3-legend.susielu.com

See document under ./paplot/lib/.