paplot documentation

Contents:

start-up guide

• About
  • Available reports
• Quick Start
  • 1. Install paplot
  • 2. Execute paplot with simple example data
  • 3. View the output file
• Install
  • For Linux
  • For MacOS X
  • For Windows
• paplot command
  • 1. Basic usage
  • 2. Output directory
  • 3. Options

how to use graphs

• Quality Control (QC) Report
• Chromosomal Aberration (CA) Report
• Mutation Matrix Report
  • 1. X-axis sort
  • 2. Y-axis sort
  • 3. Sample filter
  • 4. Genes filter
• Mutational Signature Report

data format

• QC Report
  • 1. Minimal dataset
  • 2. Without header
  • 3. Stacked bargraph
  • 4. Various graphs
  • 5. Graph for selecting samples
• Chromosomal Aberration Report
  • 1. Minimal dataset
  • 2. Without header
  • 3. Customizing categorization
  • 4. Customizing pop-up information
• Mutation Matrix Report
  • 1. Minimal dataset
  • 2. Without header
  • 3. Customizing pop-up information
• Mutational Signature Report
  • 1. Input data format
  • 2. Minimal dataset
  • 3. Mutation signature with multiple numbers of signatures
  • 4. Signature contribution graph
• pmsignature Report
  • 1. Input data format
  • 2. Minimal dataset
  • 3. Mutation signature with multiple numbers of signatures
  • 4. Signature contribution graph
  • 5. Without background
• Common Issues
  • 1. Delimiter for the input data
  • 2. Comment line
  • 3. Processing multiple input data
  • 4. Keyword
  • 5. User defined format

information

• Release Note
• License
• Contact

Javascript Libraries

paplot uses the following javascript packages.

• D3.js
• d3-legend