paplot creates various dynamic and interactive reports for cancer genome analysis.
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README.md

Build Status Quality Gate PyPI version Python Python License Documentation status

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/


2. Documentation

English:

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

Japanese:

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


3. Dependency

  • python >= 2.7

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

  • Firefox 48
  • Google Chrome 44
  • Internet Explorer 11

4. Install

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

python setup.py build install --user

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.

See document under ./paplot/lib/.