data-visualization
# Data Visualization This Claude Code skill provides guidance on selecting appropriate chart types for different data relationships, Python code patterns for matplotlib, seaborn, and plotly visualization libraries, and design principles including accessibility and color theory considerations. Use it when building charts, determining the best visualization type for a dataset, creating publication-quality figures, or applying best practices for effective data communication.
git clone --depth 1 https://github.com/openyak/openyak /tmp/data-visualization && cp -r /tmp/data-visualization/backend/app/data/plugins/data/skills/data-visualization ~/.claude/skills/data-visualizationSKILL.md
# Data Visualization Skill
Chart selection guidance, Python visualization code patterns, design principles, and accessibility considerations for creating effective data visualizations.
## Chart Selection Guide
### Choose by Data Relationship
| What You're Showing | Best Chart | Alternatives |
|---|---|---|
| **Trend over time** | Line chart | Area chart (if showing cumulative or composition) |
| **Comparison across categories** | Vertical bar chart | Horizontal bar (many categories), lollipop chart |
| **Ranking** | Horizontal bar chart | Dot plot, slope chart (comparing two periods) |
| **Part-to-whole composition** | Stacked bar chart | Treemap (hierarchical), waffle chart |
| **Composition over time** | Stacked area chart | 100% stacked bar (for proportion focus) |
| **Distribution** | Histogram | Box plot (comparing groups), violin plot, strip plot |
| **Correlation (2 variables)** | Scatter plot | Bubble chart (add 3rd variable as size) |
| **Correlation (many variables)** | Heatmap (correlation matrix) | Pair plot |
| **Geographic patterns** | Choropleth map | Bubble map, hex map |
| **Flow / process** | Sankey diagram | Funnel chart (sequential stages) |
| **Relationship network** | Network graph | Chord diagram |
| **Performance vs. target** | Bullet chart | Gauge (single KPI only) |
| **Multiple KPIs at once** | Small multiples | Dashboard with separate charts |
### When NOT to Use Certain Charts
- **Pie charts**: Avoid unless <6 categories and exact proportions matter less than rough comparison. Humans are bad at comparing angles. Use bar charts instead.
- **3D charts**: Never. They distort perception and add no information.
- **Dual-axis charts**: Use cautiously. They can mislead by implying correlation. Clearly label both axes if used.
- **Stacked bar (many categories)**: Hard to compare middle segments. Use small multiples or grouped bars instead.
- **Donut charts**: Slightly better than pie charts but same fundamental issues. Use for single KPI display at most.
## Python Visualization Code Patterns
### Setup and Style
```python
import matplotlib.pyplot as plt
import matplotlib.ticker as mticker
import seaborn as sns
import pandas as pd
import numpy as np
# Professional style setup
plt.style.use('seaborn-v0_8-whitegrid')
plt.rcParams.update({
'figure.figsize': (10, 6),
'figure.dpi': 150,
'font.size': 11,
'axes.titlesize': 14,
'axes.titleweight': 'bold',
'axes.labelsize': 11,
'xtick.labelsize': 10,
'ytick.labelsize': 10,
'legend.fontsize': 10,
'figure.titlesize': 16,
})
# Colorblind-friendly palettes
PALETTE_CATEGORICAL = ['#4C72B0', '#DD8452', '#55A868', '#C44E52', '#8172B3', '#937860']
PALETTE_SEQUENTIAL = 'YlOrRd'
PALETTE_DIVERGING = 'RdBu_r'
```
### Line Chart (Time Series)
```python
fig, ax = plt.subplots(figsize=(10, 6))
for label, group in df.groupby('category'):
ax.plot(group['date'], group['value'], label=label, linewidth=2)
ax.set_title('Metric Trend by Category', fontweight='bold')
ax.set_xlabel('Date')
ax.set_ylabel('Value')
ax.legend(loc='upper left', frameon=True)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
# Format dates on x-axis
fig.autofmt_xdate()
plt.tight_layout()
plt.savefig('trend_chart.png', dpi=150, bbox_inches='tight')
```
### Bar Chart (Comparison)
```python
fig, ax = plt.subplots(figsize=(10, 6))
# Sort by value for easy reading
df_sorted = df.sort_values('metric', ascending=True)
bars = ax.barh(df_sorted['category'], df_sorted['metric'], color=PALETTE_CATEGORICAL[0])
# Add value labels
for bar in bars:
width = bar.get_width()
ax.text(width + 0.5, bar.get_y() + bar.get_height()/2,
f'{width:,.0f}', ha='left', va='center', fontsize=10)
ax.set_title('Metric by Category (Ranked)', fontweight='bold')
ax.set_xlabel('Metric Value')
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
plt.tight_layout()
plt.savefig('bar_chart.png', dpi=150, bbox_inches='tight')
```
### Histogram (Distribution)
```python
fig, ax = plt.subplots(figsize=(10, 6))
ax.hist(df['value'], bins=30, color=PALETTE_CATEGORICAL[0], edgecolor='white', alpha=0.8)
# Add mean and median lines
mean_val = df['value'].mean()
median_val = df['value'].median()
ax.axvline(mean_val, color='red', linestyle='--', linewidth=1.5, label=f'Mean: {mean_val:,.1f}')
ax.axvline(median_val, color='green', linestyle='--', linewidth=1.5, label=f'Median: {median_val:,.1f}')
ax.set_title('Distribution of Values', fontweight='bold')
ax.set_xlabel('Value')
ax.set_ylabel('Frequency')
ax.legend()
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
plt.tight_layout()
plt.savefig('histogram.png', dpi=150, bbox_inches='tight')
```
### Heatmap
```python
fig, ax = plt.subplots(figsize=(10, 8))
# Pivot data for heatmap format
pivot = df.pivot_table(index='row_dim', columns='col_dim', values='metric', aggfunc='sum')
sns.heatmap(pivot, annot=True, fmt=',.0f', cmap='YlOrRd',
linewidths=0.5, ax=ax, cbar_kws={'label': 'Metric Value'})
ax.set_title('Metric by Row Dimension and Column Dimension', fontweight='bold')
ax.set_xlabel('Column Dimension')
ax.set_ylabel('Row Dimension')
plt.tight_layout()
plt.savefig('heatmap.png', dpi=150, bbox_inches='tight')
```
### Small Multiples
```python
categories = df['category'].unique()
n_cats = len(categories)
n_cols = min(3, n_cats)
n_rows = (n_cats + n_cols - 1) // n_cols
fig, axes = plt.subplots(n_rows, n_cols, figsize=(5*n_cols, 4*n_rows), sharex=True, sharey=True)
axes = axes.flatten() if n_cats > 1 else [axes]
for i, cat in enumerate(categories):
ax = axes[i]
subset = df[df['category'] == cat]
ax.plot(subset['date'], subset['value'], color=PALETTE_CATEGORICAL[i % len(PALETTE_CATEGORICAL)])
ax.set_title(cat, fontsize=12)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
# Hide empty subplots
for j in range(i+1, len(axes)):
axes[j].set_visible(False)Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines.
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP servers are connected, or surveying available analysis skills before starting a new project.
>
>