plotly-for-scanpy

Interactive Plotly-based visualization tools for Scanpy single-cell data analysis, providing drop-in alternatives to scanpy.pl functions with enhanced interactivity.

Installation

pip install plotly-for-scanpy

Features

• Dynamic Downsampling: Efficiently visualize large datasets with intelligent point reduction
• Interactive Plots: All visualizations are fully interactive with zoom, pan, and hover functionality
• Scanpy Integration: Works seamlessly with AnnData objects
• Publication Quality: Easily export to HTML or static formats

Example Usage

import scanpy as sc
import plotly_for_scanpy as psc

# Load data
adata = sc.datasets.pbmc3k()
sc.pp.normalize_total(adata)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata)
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata)

# Use interactive UMAP visualization
psc.umap(adata, color=['leiden'])

# Visualize with dynamic downsampling for large datasets
fig = psc.umap(adata, color='leiden', return_fig=True)
dynamic_fig = psc.dd(fig, resolution=10000)
dynamic_fig.show()

Documentation

Full examples and tutorials:

• Interactive Colab Demo

License

MIT License