bio-data-visualization-interactive-visualization

Version Compatibility

Reference examples tested with: ggplot2 3.5+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to 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.

Interactive Visualization

"Create interactive plots" → Build zoomable, hoverable visualizations for exploring large datasets in notebooks or HTML reports.

• Python: plotly.express, bokeh, altair
• R: plotly::ggplotly(), htmlwidgets

plotly (Python)

import plotly.express as px
import plotly.graph_objects as go
import pandas as pd

# Scatter plot
fig = px.scatter(df, x='PC1', y='PC2', color='condition', hover_data=['sample'],
                 title='PCA Plot')
fig.write_html('pca_interactive.html')
fig.show()

Interactive Volcano Plot

Goal: Create a zoomable, hoverable volcano plot for exploring differential expression results.

Approach: Compute significance categories, build a plotly scatter with gene names on hover and metadata tooltips, add threshold reference lines, and export as standalone HTML.

import plotly.express as px

df['neg_log_pval'] = -np.log10(df['pvalue'])
df['significant'] = (df['padj'] < 0.05) & (abs(df['log2FoldChange']) > 1)

fig = px.scatter(df, x='log2FoldChange', y='neg_log_pval',
                 color='significant', hover_name='gene',
                 hover_data=['baseMean', 'padj'],
                 color_discrete_map={True: 'red', False: 'grey'},
                 title='Interactive Volcano Plot')

fig.add_hline(y=-np.log10(0.05), line_dash='dash', line_color='grey')
fig.add_vline(x=-1, line_dash='dash', line_color='grey')
fig.add_vline(x=1, line_dash='dash', line_color='grey')

fig.update_layout(xaxis_title='Log2 Fold Change', yaxis_title='-Log10 P-value')
fig.write_html('volcano_interactive.html')