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:
|
---|---|
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 |