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-circos-plotsnpx skills add thesecondfox/skill --skill bio-data-visualization-circos-plotsgit 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-circos-plots)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-data-visualization-circos-plots"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-data-visualization-circos-plots.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 | $0.00051 | $0.03101 |
| Opus 5 | $0.00026 | $0.01550 |
| Sonnet 5 | $0.00010 | $0.00620 |
| Haiku 4.5 | $0.00005 | $0.00310 |
Grade A, and why
bio-data-visualization-circos-plots 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 3d 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 — 406 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pandas 2.2+
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 - CLI:
<tool> --versionthen<tool> --helpto 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.
Circos Plots
"Create a circos plot" → Visualize genomic data in a circular layout showing chromosomes, links, and data tracks.
- Python:
pycircos,pyCirclize(Python circular layout) - R:
circlize::chordDiagram(),circlize::circos.genomicTrack()
Circular genome visualizations for displaying multiple data tracks around chromosome ideograms.
Tool Options
| Tool | Language | Best For |
|---|---|---|
| Circos | Perl/CLI | Publication-quality, complex layouts |
| pyCircos | Python | Programmatic generation, integration |
| circlize | R | Quick plots, Bioconductor integration |
Circos (Original)
Installation
conda install -c bioconda circos
# Or download from http://circos.ca
Basic Configuration
Circos requires configuration files defining the plot structure.
circos.conf (main config)
# Chromosome definitions
karyotype = data/karyotype.human.hg38.txt
<ideogram>
<spacing>
default = 0.005r
</spacing>
radius = 0.90r
thickness = 20p
fill = yes
</ideogram>
<image>
dir = output
file = circos.png
png = yes
svg = yes
radius = 1500p
</image>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
Data Tracks
Scatter Plot Track
<plots>
<plot>
type = scatter
file = data/scatter.txt
r0 = 0.75r
r1 = 0.85r
min = 0
max = 1
glyph = circle
glyph_size = 8p
color = red
</plot>
</plots>
Histogram Track
<plot>
type = histogram
file = data/histogram.txt
r0 = 0.60r
r1 = 0.74r
min = 0
max = 100
fill_color = blue
</plot>
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.
- 3d ago First seen · 406 lines · 51 tokens per session scan A 07c136d72df4
bio-data-visualization-circos-plots is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 51 tokens to every session and 3,101 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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