bio-metagenomics-visualization
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-visualization --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: MetaPhlAn 4.1+, ggplot2 3.5+, matplotlib 3.8+, pandas 2.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+, scipy 1.12+, seaborn 0.13+, vegan 2.6+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Metagenome Visualization **"Visualize the taxonomic composition of my metagenomes"** → Create publication-quality figures (stacked bars, heatmaps, ordination plots) from taxonomic profiling output to compare community composition across samples. - R: `phyloseq::plot_bar()`, `microbiome` package - Python: `matplotlib`/`seaborn` with pandas for custom compositions ## Python - Stacked Bar Plot ```python import pandas as pd import matplotlib.pyplot as plt abundance = pd.read_csv('merged_abundance.txt', sep='\t', index_col=0) abundanc
- Version Compatibility
- Python - Stacked Bar Plot
- Python - Heatmap
- Python - PCA
- R - phyloseq Setup
- R - Stacked Bar Plot
- R - Ordination (PCoA)
- R - Alpha Diversity
- R - Beta Diversity (PERMANOVA)
- Krona Chart
- Key Packages
- Python
- R
- Related Skills
From Kraken2 report ktImportTaxonomy -q 1 -t 5 kraken_report.txt -o krona_chart.html From MetaPhlAn metaphlan2krona.py -p profile.txt -k krona_profile.txt ktImportText krona_profile.txt -o krona_metaphlan.html
What does the bio-metagenomics-visualization skill do?
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metagenomics-visualization --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.