plot-roh-py

name	plot-roh-py
description	Use when plotting runs of homozygosity from `run-roh.pl` style output directories into PNG tracks, optionally filtered by region, sample list, or group contrast.
disable-model-invocation	true
user-invocable	true

plot-roh-py

Python plotting script for ROH visualization. It scans a directory of *.txt.gz files, reads both GT and RG records, and renders per-sample ROH tracks to plot.png or a user-specified output file.

Quick Start

• Command: plot-roh.py <dir>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/plot-roh.py
• Default output: plot.png

When To Use This Tool

• Visualizing ROH calls that have already been converted into the GT/RG text format expected by the script
• Rendering static PNG ROH track plots without writing custom matplotlib code
• Filtering ROH calls by minimum length, marker count, quality, or genomic region
• Comparing grouped samples with --highlight +group1,-group2

Common Patterns

# Basic non-interactive plot
plot-roh.py roh_dir -o roh.png

# Restrict plotted calls by region and quality/length filters
plot-roh.py roh_dir -r chr1:1-5000000 -l 100000 -n 20 -q 30 -o chr1.png

# Use a sample/group file and highlight calls enriched in one group
plot-roh.py roh_dir -s samples.tsv -H +cases,-controls -o grouped.png

Recommended Workflow

1. Feed the script a directory containing gzipped text files with both GT genotype rows and RG region rows.
2. Use -o for batch output or -i for interactive plotting, but not both.
3. Add -s when you need renaming or grouping, then layer -H on top for between-group highlighting.
4. Tighten -l, -n, -q, and -r before plotting large cohorts so the rendered track view stays readable.

Guardrails

• The script does not accept raw bcftools roh output by itself; the source explicitly says it expects extra GT lines such as those produced by run-roh.pl.
• A directory with only RG rows failed in live testing with IndexError: list index out of range because RG rows must include at least eight columns, including quality.
• A minimal gzipped file containing two GT rows plus one RG row successfully produced a PNG (3000 x 150) in local testing.
• --version is not a real metadata path; running it without a valid data directory falls through to No data files found in "--version".
• -i/--interactive and -o/--outfile are mutually exclusive, and the script will exit with a usage error if both are provided.