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beta_jitter_plot.rst

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beta_jitter_plot.py

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.
  • 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.

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.

Input files (examples)

Command

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

Output files

  • Jitter.r
  • Jitter.pdf

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