10. beta_jitter_plot.py

10.1. Description

This program generates jitter plot (a.k.a. strip chart) and bean plot for each sample (column)

Example of input

CpG_ID  Sample_01       Sample_02       Sample_03       Sample_04
cg_001  0.831035        0.878022        0.794427        0.880911
cg_002  0.249544        0.209949        0.234294        0.236680
cg_003  0.845065        0.843957        0.840184        0.824286

Notes

  • User must install the beanplot R library.

10.2. Options

--version

show program’s version number and exit

-h, --help

show this help message and exit

-i INPUT_FILE, --input_file=INPUT_FILE

Tab-separated data frame file containing beta values with the 1st row containing sample IDs and the 1st column containing CpG IDs.

-f FRACTION, --fraction=FRACTION

The fraction of total data points (CpGs) used to generate jitter plot. Decrease this number if the jitter plot is over-crowded. default=0.5

-o OUT_FILE, --output=OUT_FILE

The prefix of the output file.

10.3. Input files (examples)

10.4. Command

$beta_jitterPlot.py -f 1 -i test_05_TwoGroup.tsv.gz -o Jitter

10.5. Output files

  • Jitter.r

  • Jitter.pdf

../_images/Jitter.png