How do I install the Plot Roh Py skill?

Run npx skillmds add vimalinx/plot-roh-py in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

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Is Plot Roh Py free to use?

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Who published Plot Roh Py?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Plot Roh Py by vimalinx — Agent Skill

Name: Plot Roh Py
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

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

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.

---name: plot-roh-pydescription: 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.--- # 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 ```bash # Basic non-interactive plot plot-roh.py roh_dir -o roh.png ``` ```bash # 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 ``` ```bash # 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.

Frequently asked questions