README.md

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] [--config_file CONFIG_FILE] [--title TITLE]
                 [--ellipsis ELLIPSIS] [--overview OVERVIEW]
                 [--remarks REMARKS]
                 input output_dir project_name

positional arguments:
  input                 input files path
  output_dir            output file path
  project_name          project name

optional arguments:
  -h, --help            show this help message and exit
  --config_file CONFIG_FILE
                        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] [--config_file CONFIG_FILE] [--title TITLE]
                 [--ellipsis ELLIPSIS] [--overview OVERVIEW]
                 [--remarks REMARKS]
                 input output_dir project_name

positional arguments:
  input                 input files path
  output_dir            output file path
  project_name          project name

optional arguments:
  -h, --help            show this help message and exit
  --config_file CONFIG_FILE
                        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] [--config_file CONFIG_FILE] [--title TITLE]
                       [--ellipsis ELLIPSIS] [--overview OVERVIEW]
                       [--remarks REMARKS]
                       input output_dir project_name

positional arguments:
  input                 input files path
  output_dir            output file path
  project_name          project name

optional arguments:
  -h, --help            show this help message and exit
  --config_file CONFIG_FILE
                        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] [--config_file CONFIG_FILE] [--title TITLE]
                        [--ellipsis ELLIPSIS] [--overview OVERVIEW]
                        [--remarks REMARKS]
                        input output_dir project_name

positional arguments:
  input                 input files path
  output_dir            output file path
  project_name          project name

optional arguments:
  -h, --help            show this help message and exit
  --config_file CONFIG_FILE
                        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] [--config_file CONFIG_FILE] [--title TITLE]
                          [--ellipsis ELLIPSIS] [--overview OVERVIEW]
                          [--remarks REMARKS]
                          input output_dir project_name

positional arguments:
  input                 input files path
  output_dir            output file path
  project_name          project name

optional arguments:
  -h, --help            show this help message and exit
  --config_file CONFIG_FILE
                        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/.