12. beta_jitter_plot.py

12.1. 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


  • User must install the beanplot R library.
  • Please name your sample IDs (such as “Sample_01”, “Sample_02” in the above example) using only “letters” [a-z, A-Z], “numbers” [0-9], and “_”; and your sample ID must start with a letter.

12.2. 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.

12.3. Input files (examples)

12.4. Command

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

12.5. Output files

  • Jitter.r
  • Jitter.pdf