20. beta_stacked_barplot

20.1. Overview

beta_stacked_barplot summarizes the distribution of Beta-values for each sample and optionally generates a stacked bar plot.

The input matrix should have CpGs in rows and samples in columns.

Beta-values are grouped into four intervals:

• [0.00, 0.25]

• (0.25, 0.50]

• (0.50, 0.75]

• (0.75, 1.00]

20.2. Input

The input is a tabular Beta-value matrix. Delimiters are detected automatically and compressed input is supported.

Example:

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

By default, finite values outside [0, 1] cause an error.

20.3. Usage

Basic usage:

beta_stacked_barplot \
    -i cirrHCV_vs_normal.data.tsv \
    -o stacked_bar

Useful options include:

• --format {png,pdf,both} – plot format (default: pdf)

• --dpi – PNG resolution (default: 300)

• --width and --height – plot size in inches

• --no_plot – write only the summary table

• --allow_out_of_range – ignore finite values outside [0, 1]

Display all options with:

beta_stacked_barplot -h

20.4. Output

For output prefix stacked_bar, the command writes:

• stacked_bar.stacked_barplot.tsv – counts and percentages for each sample and Beta-value interval

• stacked_bar.stacked_barplot.pdf – plot when --format pdf is used

• stacked_bar.stacked_barplot.png – plot when --format png is used

Use --format both to generate both plot formats.

20.5. Example Data

• cirrHCV_vs_normal.data.tsv

20.6. Example Figure