13. beta_stacked_barplot.py

13.1. Description

This program creates stacked barplot for each sample. The stacked barplot showing the proportions of CpGs whose beta values are falling into these 4 ranges: 1. [0.00, 0.25] #first quantile 2. [0.25, 0.50] #second quantile 3. [0.50, 0.75] #third quantile 4. [0.75, 1.00] #forth quantile

Example of input file

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

13.2. Options

--version

show program’s version number and exit

-h, --help

show this help message and exit

-i INPUT_FILE, --input-file-INPUT_FILE

Data frame file containing beta values with the 1st row containing sample IDs and the 1st column containing CpG IDs.

-o OUT_FILE, --output-OUT_FILE

Prefix of the output file.

13.3. Input files (examples)

13.4. Command

$beta_stacked_barplot.py -i cirrHCV_vs_normal.data.tsv -o stacked_bar

13.5. Output files

  • stacked_bar.r

  • stacked_bar.pdf

../_images/stacked_bar.png