15. beta_jitter_plot

15.1. Overview

beta_jitter_plot visualizes DNA methylation Beta-value distributions for each sample using a jitter (strip) plot overlaid with a bean plot.

The input matrix should have CpGs in rows and samples in columns. Plotting is performed with R and the beanplot package.

15.2. Requirements

The command requires:

• Rscript available in PATH

• the R package beanplot

15.3. Input

The input must be a tab-delimited Beta-value matrix. 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
cg_003   0.845065    0.843957    0.840184    0.824286

Sample IDs must be unique. Non-numeric values are treated as missing values. Values outside the expected [0, 1] Beta-value range are retained, but a warning is reported.

Example data:

• test_05_TwoGroup.tsv.gz

15.4. Usage

Basic usage:

beta_jitter_plot \
    -i test_05_TwoGroup.tsv.gz \
    -f 1 \
    -o Jitter

Useful options include:

• -f, --fraction – fraction of CpGs plotted; must be in (0, 1] (default: 0.5)

• --seed – random seed used when subsampling CpGs (default: 999)

• --width – output PNG width in pixels (default: 800)

• --height – output PNG height in pixels (default: 480)

• --point_size – jitter-point size multiplier (default: 0.1)

• --jitter – horizontal jitter width (default: 0.3)

• --keep_plot_data – retain the sampled CpG matrix used for plotting

• -o, --out_prefix, --output – output prefix

Display all options with:

beta_jitter_plot -h

15.5. Output

For output prefix Jitter, the command generates:

• Jitter.r – R script used to generate the plot

• Jitter.png – jitter/bean plot

The intermediate file Jitter.plot_data.tsv is removed after plotting by default. Use --keep_plot_data to retain it.

15.6. Example Figure