paplot command

1. Basic usage

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

Required arguments

subcommand:

The type of report to generate. Select from the following:

• qc
• ca
• mutation
• signature
• pmsignature

input:

Input files. If you wish to process multiple files (usually divided by individual samples), please refer to Processing multiple input files.

# for single input file
paplot mutation {unzip_path}/example/mutation_minimal/data.csv ./tmp mutation_minimal \
--config_file {unzip_path}/example/mutation_minimal/paplot.cfg

# for multiple input files, delimit them by comma
paplot mutation \
{unzip_path}/example/mutation_split_file/SAMPLE00.data.csv,{unzip_path}/example/mutation_split_file/SAMPLE01.data.csv \
./tmp mutation_split_file1 --config_file {unzip_path}/example/mutation_split_file/paplot.cfg

# paplot also accept wild card representation. In this case enclose the input by double quotations
paplot mutation "{unzip_path}/example/mutation_split_file/*.csv" ./tmp mutation_split_file2 \
--config_file {unzip_path}/example/mutation_split_file/paplot.cfg

output_dir:Output directory path. Refer Output directory for the details of the directory components. project_name:Project name (used as the title of the output files).

2. Output directory

You will find the following directory structure:

{output_dir}
  ├ {project_name}
  │   └ graph_*.html      <--- Each report
  │
  ├ js          <--- The next four directories are necessary to display HTML files, Do not remove them.
  ├ layout
  ├ lib
  ├ style
  │
  └ index.html             <--- Open this file in a web browser.

If you wish to move the output, move the entire output directory. For the usage of each report, please refer to HOW TO USE GRAPHS.

3. Options

You can add the following optional arguments:

--config_file	Path to the configuration file. If it is not specified, the default file is used.
--title	Title of the graph.
--ellipsis	Abbreviated name of the graph used for file names (e.g., graph_**ca**.html). It may be convenient when outputting multiple files to the same directory.
--overview	Outline of the graph (displayed in the index.html file).
--remarks	Text displayed in the remark section of the index.html file (the default value is set at ( [style] section’s remarks option) in the configuration file.

The default values are as follows:

subcommand	title	ellipsis	overview	remarks
qc	QC graphs	qc	Quality Control of bam.	None
ca	CA graphs	ca	Chromosomal Aberration.	None
mutation	Mutation Matrix	mutation	Gene-sample mutational profiles.	None
signature	Signature	signature	Mutational Signatures.	None
pmsignature	PMSignature	pmsignature	Express mutational signatures in pmsignature.	None