Data Visualization (Universal)

Overview

This skill enables you to create professional scientific visualizations including scatter plots, line charts, heatmaps, violin plots, and more. Unlike cloud-hosted solutions, this skill uses the matplotlib and seaborn Python libraries and executes locally in your environment, making it compatible with ALL LLM providers including GPT, Gemini, Claude, DeepSeek, and Qwen.

When to Use This Skill

• Create publication-quality figures for papers and presentations
• Generate exploratory data analysis (EDA) plots
• Visualize gene expression, QC metrics, or clustering results
• Create multi-panel figures combining different plot types
• Export high-resolution images for reports
• Customize plot aesthetics (colors, fonts, styles)

How to Use

Step 1: Import Required Libraries

import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import numpy as np
from matplotlib import gridspec
import matplotlib.patches as mpatches

# Set style for publication-quality plots
sns.set_style("whitegrid")
plt.rcParams['figure.dpi'] = 150
plt.rcParams['savefig.dpi'] = 300
plt.rcParams['font.size'] = 10

Step 2: Basic Scatter Plot

# Create figure and axis
fig, ax = plt.subplots(figsize=(6, 5))

# Scatter plot
ax.scatter(x_data, y_data, s=20, alpha=0.6, c='steelblue', edgecolors='k', linewidths=0.5)

# Labels and title
ax.set_xlabel('Gene Expression (log2)', fontsize=12)
ax.set_ylabel('Cell Count', fontsize=12)
ax.set_title('Expression vs. Cell Count', fontsize=14, fontweight='bold')

# Grid and styling
ax.grid(alpha=0.3)
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)

# Save figure
plt.tight_layout()
plt.savefig('scatter_plot.png', dpi=300, bbox_inches='tight')
plt.show()
print("✅ Scatter plot saved to: scatter_plot.png")

Step 3: Line Plot with Multiple Series

fig, ax = plt.subplots(figsize=(8, 5))

# Plot multiple lines
ax.plot(time_points, group1_values, marker='o', label='Group 1', color='#E74C3C', linewidth=2)
ax.plot(time_points, group2_values, marker='s', label='Group 2', color='#3498DB', linewidth=2)
ax.plot(time_points, group3_values, marker='^', label='Group 3', color='#2ECC71', linewidth=2)

# Styling
ax.set_xlabel('Time Point', fontsize=12)
ax.set_ylabel('Expression Level', fontsize=12)
ax.set_title('Gene Expression Over Time', fontsize=14, fontweight='bold')
ax.legend(frameon=True, loc='best', fontsize=10)
ax.grid(alpha=0.3, linestyle='--')

plt.tight_layout()
plt.savefig('line_plot.png', dpi=300, bbox_inches='tight')
plt.show()

Step 4: Box Plot and Violin Plot

# Prepare data (long-form DataFrame)
# df should have columns: 'cluster', 'expression', 'gene', etc.

fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5))

# Box plot
sns.boxplot(data=df, x='cluster', y='expression', palette='Set2', ax=ax1)
ax1.set_title('Box Plot: Expression by Cluster', fontsize=12, fontweight='bold')
ax1.set_xlabel('Cluster', fontsize=11)
ax1.set_ylabel('Expression Level', fontsize=11)
ax1.tick_params(axis='x', rotation=45)

# Violin plot
sns.violinplot(data=df, x='cluster', y='expression', palette='muted', ax=ax2, inner='quartile')
ax2.set_title('Violin Plot: Expression Distribution', fontsize=12, fontweight='bold')
ax2.set_xlabel('Cluster', fontsize=11)
ax2.set_ylabel('Expression Level', fontsize=11)
ax2.tick_params(axis='x', rotation=45)

plt.tight_layout()
plt.savefig('box_violin_plot.png', dpi=300, bbox_inches='tight')
plt.show()

Step 5: Heatmap

# Prepare data matrix (rows=genes, columns=samples or clusters)
# gene_expression_matrix: pandas DataFrame or numpy array

fig, ax = plt.subplots(figsize=(8, 6))

# Create heatmap
sns.heatmap(
    gene_expression_matrix,
    cmap='viridis',
    cbar_kws={'label': 'Expression'},
    xticklabels=True,
    yticklabels=True,
    linewidths=0.5,
    linecolor='gray',
    ax=ax
)

ax.set_title('Gene Expression Heatmap', fontsize=14, fontweight='bold')
ax.set_xlabel('Samples', fontsize=12)
ax.set_ylabel('Genes', fontsize=12)

plt.tight_layout()
plt.savefig('heatmap.png', dpi=300, bbox_inches='tight')
plt.show()

Step 6: Bar Plot with Error Bars

fig, ax = plt.subplots(figsize=(7, 5))

# Data
categories = ['Cluster 0', 'Cluster 1', 'Cluster 2', 'Cluster 3']
means = [120, 85, 200, 150]
errors = [15, 10, 25, 20]

# Bar plot
bars = ax.bar(categories, means, yerr=errors, capsize=5,
               color=['#E74C3C', '#3498DB', '#2ECC71', '#F39C12'],
               edgecolor='black', linewidth=1.2, alpha=0.8)

# Labels
ax.set_ylabel('Cell Count', fontsize=12)
ax.set_title('Cell Counts by Cluster', fontsize=14, fontweight='bold')
ax.set_ylim(0, max(means) * 1.3)

# Add value labels on bars
for bar, mean in zip(bars, means):
    height = bar.get_height()
    ax.text(bar.get_x() + bar.get_width()/2., height + 5,
            f'{mean}', ha='center', va='bottom', fontsize=10)

plt.tight_layout()
plt.savefig('bar_plot.png', dpi=300, bbox_inches='tight')
plt.show()

Advanced Features

Multi-Panel Figure

# Create complex layout
fig = plt.figure(figsize=(12, 8))
gs = gridspec.GridSpec(2, 3, figure=fig, hspace=0.3, wspace=0.3)

# Panel A: Scatter
ax1 = fig.add_subplot(gs[0, :2])
ax1.scatter(x_data, y_data, c=cluster_labels, cmap='tab10', s=10, alpha=0.6)
ax1.set_title('A. UMAP Projection', fontsize=12, fontweight='bold', loc='left')
ax1.set_xlabel('UMAP1')
ax1.set_ylabel('UMAP2')

# Panel B: Violin
ax2 = fig.add_subplot(gs[0, 2])
sns.violinplot(data=df, y='expression', palette='Set2', ax=ax2)
ax2.set_title('B. Expression', fontsize=12, fontweight='bold', loc='left')

# Panel C: Heatmap
ax3 = fig.add_subplot(gs[1, :])
sns.heatmap(matrix, cmap='coolwarm', center=0, ax=ax3, cbar_kws={'label': 'Z-score'})
ax3.set_title('C. Gene Expression Heatmap', fontsize=12, fontweight='bold', loc='left')

plt.savefig('multi_panel_figure.png', dpi=300, bbox_inches='tight')
plt.show()

Custom Color Palette

# Define custom colors
custom_palette = ['#E74C3C', '#3498DB', '#2ECC71', '#F39C12', '#9B59B6']

# Use in seaborn
sns.set_palette(custom_palette)

# Or create color dict for specific mapping
color_dict = {
    'T cells': '#E74C3C',
    'B cells': '#3498DB',
    'Monocytes': '#2ECC71',
    'NK cells': '#F39C12'
}

# Use in scatter plot
for cell_type, color in color_dict.items():
    mask = df['celltype'] == cell_type
    ax.scatter(df.loc[mask, 'x'], df.loc[mask, 'y'],
               c=color, label=cell_type, s=20, alpha=0.7)
ax.legend()

Density Plot

from scipy.stats import gaussian_kde

fig, ax = plt.subplots(figsize=(8, 6))

# Calculate density
xy = np.vstack([x_data, y_data])
z = gaussian_kde(xy)(xy)

# Sort points by density for better visualization
idx = z.argsort()
x, y, z = x_data[idx], y_data[idx], z[idx]

# Scatter with density colors
scatter = ax.scatter(x, y, c=z, s=20, cmap='viridis', alpha=0.6, edgecolors='none')
plt.colorbar(scatter, ax=ax, label='Density')

ax.set_xlabel('UMAP1', fontsize=12)
ax.set_ylabel('UMAP2', fontsize=12)
ax.set_title('Density Scatter Plot', fontsize=14, fontweight='bold')

plt.tight_layout()
plt.savefig('density_plot.png', dpi=300, bbox_inches='tight')
plt.show()

Common Use Cases

QC Metrics Visualization

# Assuming adata.obs has QC columns: n_genes, n_counts, percent_mito

fig, axes = plt.subplots(1, 3, figsize=(15, 4))

# Plot 1: Histogram of genes per cell
axes[0].hist(adata.obs['n_genes'], bins=50, color='steelblue', edgecolor='black', alpha=0.7)
axes[0].axvline(adata.obs['n_genes'].median(), color='red', linestyle='--', label='Median')
axes[0].set_xlabel('Genes per Cell', fontsize=11)
axes[0].set_ylabel('Frequency', fontsize=11)
axes[0].set_title('Genes per Cell Distribution', fontsize=12, fontweight='bold')
axes[0].legend()

# Plot 2: Scatter UMI vs Genes
axes[1].scatter(adata.obs['n_counts'], adata.obs['n_genes'],
                s=5, alpha=0.5, c='coral')
axes[1].set_xlabel('UMI Counts', fontsize=11)
axes[1].set_ylabel('Genes Detected', fontsize=11)
axes[1].set_title('UMIs vs Genes', fontsize=12, fontweight='bold')

# Plot 3: Violin plot of mitochondrial percentage
sns.violinplot(y=adata.obs['percent_mito'], ax=axes[2], color='lightgreen')
axes[2].axhline(y=20, color='red', linestyle='--', label='20% threshold')
axes[2].set_ylabel('Mitochondrial %', fontsize=11)
axes[2].set_title('Mitochondrial Content', fontsize=12, fontweight='bold')
axes[2].legend()

plt.tight_layout()
plt.savefig('qc_metrics.png', dpi=300, bbox_inches='tight')
plt.show()

UMAP/tSNE Visualization

# Assuming adata.obsm['X_umap'] exists and adata.obs['clusters'] exists

fig, ax = plt.subplots(figsize=(8, 7))

# Get unique clusters
clusters = adata.obs['clusters'].unique()
n_clusters = len(clusters)

# Generate colors
colors = plt.cm.tab20(np.linspace(0, 1, n_clusters))

# Plot each cluster
for i, cluster in enumerate(clusters):
    mask = adata.obs['clusters'] == cluster
    ax.scatter(
        adata.obsm['X_umap'][mask, 0],
        adata.obsm['X_umap'][mask, 1],
        c=[colors[i]],
        label=f'Cluster {cluster}',
        s=10,
        alpha=0.7,
        edgecolors='none'
    )

ax.set_xlabel('UMAP1', fontsize=12)
ax.set_ylabel('UMAP2', fontsize=12)
ax.set_title('UMAP Projection by Cluster', fontsize=14, fontweight='bold')
ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left', frameon=True, fontsize=9)

plt.tight_layout()
plt.savefig('umap_clusters.png', dpi=300, bbox_inches='tight')
plt.show()

Gene Expression Dot Plot

# genes: list of gene names
# clusters: list of cluster IDs
# Create matrix: rows=genes, columns=clusters with mean expression and % expressing

fig, ax = plt.subplots(figsize=(10, 6))

# Prepare data
from matplotlib.colors import Normalize

# dot_size_matrix: % cells expressing (0-100)
# color_matrix: mean expression level

for i, gene in enumerate(genes):
    for j, cluster in enumerate(clusters):
        # Size proportional to % expressing
        size = dot_size_matrix[i, j] * 5  # Scale factor
        # Color by expression level
        color_val = color_matrix[i, j]

        ax.scatter(j, i, s=size, c=[color_val], cmap='Reds',
                   vmin=0, vmax=color_matrix.max(),
                   edgecolors='black', linewidths=0.5)

# Labels
ax.set_xticks(range(len(clusters)))
ax.set_xticklabels(clusters, rotation=45, ha='right')
ax.set_yticks(range(len(genes)))
ax.set_yticklabels(genes)
ax.set_xlabel('Cluster', fontsize=12)
ax.set_ylabel('Gene', fontsize=12)
ax.set_title('Marker Gene Expression', fontsize=14, fontweight='bold')

# Colorbar
norm = Normalize(vmin=0, vmax=color_matrix.max())
sm = plt.cm.ScalarMappable(cmap='Reds', norm=norm)
sm.set_array([])
cbar = plt.colorbar(sm, ax=ax, pad=0.02)
cbar.set_label('Mean Expression', rotation=270, labelpad=15)

plt.tight_layout()
plt.savefig('gene_dotplot.png', dpi=300, bbox_inches='tight')
plt.show()

Volcano Plot (DEG Analysis)

# Assuming deg_df has columns: gene, log2FC, pvalue

fig, ax = plt.subplots(figsize=(8, 7))

# Calculate -log10(pvalue)
deg_df['-log10_pvalue'] = -np.log10(deg_df['pvalue'])

# Classify genes
deg_df['significant'] = 'Not Significant'
deg_df.loc[(deg_df['log2FC'] > 1) & (deg_df['pvalue'] < 0.05), 'significant'] = 'Up-regulated'
deg_df.loc[(deg_df['log2FC'] < -1) & (deg_df['pvalue'] < 0.05), 'significant'] = 'Down-regulated'

# Plot
for category, color in zip(['Not Significant', 'Up-regulated', 'Down-regulated'],
                            ['gray', 'red', 'blue']):
    mask = deg_df['significant'] == category
    ax.scatter(deg_df.loc[mask, 'log2FC'],
               deg_df.loc[mask, '-log10_pvalue'],
               c=color, label=category, s=20, alpha=0.6, edgecolors='none')

# Threshold lines
ax.axvline(x=1, color='black', linestyle='--', linewidth=1, alpha=0.5)
ax.axvline(x=-1, color='black', linestyle='--', linewidth=1, alpha=0.5)
ax.axhline(y=-np.log10(0.05), color='black', linestyle='--', linewidth=1, alpha=0.5)

# Labels
ax.set_xlabel('log2 Fold Change', fontsize=12)
ax.set_ylabel('-log10(p-value)', fontsize=12)
ax.set_title('Volcano Plot: Differential Expression', fontsize=14, fontweight='bold')
ax.legend(frameon=True, loc='upper right')

plt.tight_layout()
plt.savefig('volcano_plot.png', dpi=300, bbox_inches='tight')
plt.show()

Best Practices

1. Figure Size: Use appropriate dimensions for target medium (papers: 6-8 inches wide, posters: larger)
2. DPI: Save at 300 DPI for publications, 150 DPI for presentations
3. Colors: Use colorblind-friendly palettes (e.g., viridis, Set2, tab10)
4. Fonts: Keep font sizes readable (titles: 12-14pt, labels: 10-12pt, ticks: 8-10pt)
5. Transparency: Use alpha for overlapping points to show density
6. Layout: Always call plt.tight_layout() before saving to prevent label clipping
7. File Format: PNG for general use, SVG for vector graphics (editable in Illustrator)
8. Close Figures: Call plt.close() after saving to free memory when generating many plots

Troubleshooting

Issue: "Figure too cluttered with many points"

Solution: Use transparency and smaller point sizes

ax.scatter(x, y, s=5, alpha=0.3, edgecolors='none')

Issue: "Legend overlaps with data"

Solution: Place legend outside the plot area

ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left')

Issue: "Labels are cut off in saved figure"

Solution: Use bbox_inches='tight'

plt.savefig('plot.png', dpi=300, bbox_inches='tight')

Issue: "Colors don't match between plots"

Solution: Define color palette once and reuse

PALETTE = {'Group A': '#E74C3C', 'Group B': '#3498DB'}
# Use PALETTE in all plots

Issue: "Heatmap text too small"

Solution: Adjust figure size or font size

fig, ax = plt.subplots(figsize=(12, 10))
sns.heatmap(data, ax=ax, annot_kws={'fontsize': 8})

Technical Notes

• Libraries: Uses matplotlib and seaborn (widely supported, stable)
• Execution: Runs locally in the agent's sandbox
• Compatibility: Works with ALL LLM providers (GPT, Gemini, Claude, DeepSeek, Qwen, etc.)
• File Formats: Supports PNG, PDF, SVG, JPEG
• Performance: Typical plot generation takes <1 second for standard plots, 2-5 seconds for complex multi-panel figures
• Memory: Keep figure count reasonable; close figures after saving if generating many plots

References

• Matplotlib documentation: https://matplotlib.org/stable/contents.html
• Seaborn documentation: https://seaborn.pydata.org/
• Matplotlib gallery: https://matplotlib.org/stable/gallery/index.html
• Seaborn gallery: https://seaborn.pydata.org/examples/index.html