| 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
plot-roh.py roh_dir -o roh.png
plot-roh.py roh_dir -r chr1:1-5000000 -l 100000 -n 20 -q 30 -o chr1.png
plot-roh.py roh_dir -s samples.tsv -H +cases,-controls -o grouped.png
Recommended Workflow
- Feed the script a directory containing gzipped text files with both
GT genotype rows and RG region rows.
- Use
-o for batch output or -i for interactive plotting, but not both.
- Add
-s when you need renaming or grouping, then layer -H on top for between-group highlighting.
- 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.
