plotting_guide

Comprehensive guide for creating publication-quality visualizations with scanpy.

Skills
Scientific
4

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

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Install (Claude Code)

mkdir -p .claude/skills/plotting-guide && curl -fsSL https://doutorai.pt/data/lib/skills__plotting-guide.md -o .claude/skills/plotting-guide/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

# Scanpy Plotting Guide

Comprehensive guide for creating publication-quality visualizations with scanpy.

## General Plotting Principles

All scanpy plotting functions follow consistent patterns:
- Functions in `sc.pl.*` mirror analysis functions in `sc.tl.*`
- Most accept `color` parameter for gene names or metadata columns
- Results are saved via `save` parameter
- Multiple plots can be generated in a single call

## Essential Quality Control Plots

### Visualize QC Metrics

```python
# Violin plots for QC metrics
sc.pl.violin(adata, ['n_genes_by_counts', 'total_counts', 'pct_counts_mt'],
 

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