16. beta_stacked_barplot.py¶
16.1. Description¶
This program creates stacked barplot for each sample. The stacked barplot showing the proportions of CpGs whose beta values are falling into these four ranges:
- [0.00, 0.25] #first quantile
- [0.25, 0.50] #second quantile
- [0.50, 0.75] #third quantile
- [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
Notes
- 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.
16.2. Options¶
- 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 The prefix of the output file.
16.3. Input files (examples)¶
16.4. Command¶
$beta_stacked_barplot.py -i cirrHCV_vs_normal.data.tsv -o stacked_bar