Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/thesecondfox/skill/bio-data-visualization-heatmaps-clusteringnpx skills add thesecondfox/skill --skill bio-data-visualization-heatmaps-clusteringgit clone --depth 1 https://github.com/thesecondfox/skillWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-data-visualization-heatmaps-clustering)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-data-visualization-heatmaps-clustering"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-data-visualization-heatmaps-clustering.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00057 | $0.01837 |
| Opus 5 | $0.00028 | $0.00919 |
| Sonnet 5 | $0.00011 | $0.00367 |
| Haiku 4.5 | $0.00006 | $0.00184 |
Grade A, and why
bio-data-visualization-heatmaps-clustering scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 227 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: ggplot2 3.5+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, seaborn 0.13+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - R:
packageVersion('<pkg>')then?function_nameto verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Heatmaps and Clustering
"Create a clustered heatmap" → Visualize expression matrices or distance matrices with hierarchical clustering dendrograms.
- R:
pheatmap::pheatmap(mat),ComplexHeatmap::Heatmap(mat) - Python:
seaborn.clustermap(df),scanpy.pl.heatmap(adata)
pheatmap (R) - Quick Heatmaps
library(pheatmap)
library(RColorBrewer)
# Basic heatmap with clustering
pheatmap(mat, scale = 'row', cluster_rows = TRUE, cluster_cols = TRUE)
# With annotations
annotation_col <- data.frame(
Condition = metadata$condition,
Batch = metadata$batch,
row.names = colnames(mat)
)
annotation_row <- data.frame(
Pathway = gene_info$pathway,
row.names = rownames(mat)
)
pheatmap(mat, scale = 'row',
annotation_col = annotation_col,
annotation_row = annotation_row,
color = colorRampPalette(rev(brewer.pal(9, 'RdBu')))(100),
show_rownames = FALSE,
fontsize = 8)
pheatmap Customization
# Custom annotation colors
ann_colors <- list(
Condition = c(Control = '#4DBBD5', Treatment = '#E64B35'),
Batch = c(A = '#00A087', B = '#3C5488', C = '#F39B7F'),
Pathway = c(Metabolism = '#8491B4', Signaling = '#91D1C2')
)
pheatmap(mat, scale = 'row',
annotation_col = annotation_col,
annotation_colors = ann_colors,
clustering_distance_rows = 'correlation',
clustering_distance_cols = 'euclidean',
clustering_method = 'ward.D2',
cutree_rows = 4,
cutree_cols = 2,
gaps_col = c(5, 10),
border_color = NA,
main = 'Gene Expression Heatmap')
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 4d ago First seen · 227 lines · 57 tokens per session scan A dec67b543a68
bio-data-visualization-heatmaps-clustering is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 57 tokens to every session and 1,837 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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