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bio-metagenomics-visualization
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metagenomics-visualization
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- R: phyloseq::plot_bar(), microbiome package.
- Python: matplotlib/seaborn with pandas for custom compositions.
- 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.
- abundance <- read.table('merged_abundance.txt', sep = '\t', header = TRUE, row.names = 1).
Source Doc
Excerpt From SKILL.md
R - phyloseq Setup
Goal: Convert a MetaPhlAn merged abundance table into a phyloseq object for ecological analysis and visualization in R.
Approach: Filter to species-level rows, clean taxonomy names, build an OTU table and sample metadata data frame, and assemble into a phyloseq object.
library(phyloseq)
library(ggplot2)
library(vegan)
## Filter to species level
species <- abundance[grepl('s__', rownames(abundance)), ]
rownames(species) <- sapply(strsplit(rownames(species), '\\|'), tail, 1)
rownames(species) <- gsub('s__', '', rownames(species))
## Create phyloseq object
otu <- otu_table(as.matrix(species), taxa_are_rows = TRUE)
Use cases
- Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- kraken-classification - Generate input data
- metaphlan-profiling - Generate input data
- abundance-estimation - Process Kraken output
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