plotting-embeddings

name	plotting-embeddings
description	Generate publication-quality UMAP/t-SNE embedding plots with Okabe-Ito color palette. Outputs PDF+PNG.
allowed-tools	Read, Bash
compatibility	scRNA-seq, snRNA-seq, spatial

Embedding Plots

When to Use

After clustering or annotation to visualize cell distributions.

Functions

plot_embedding(adata, embedding_key, color_by=None, output_dir=None, title=None, colors=None) -> str

Generates publication-quality embedding plot.

Parameters:

• embedding_key: "X_umap", "X_tsne", or any key in adata.obsm
• color_by: Column name in adata.obs for coloring (e.g. "leiden", "Cell#")
• output_dir: Directory to save files. If None, returns without saving
• title: Plot title. Auto-generated if None
• colors: Optional list of specific colors (uses Okabe-Ito palette by default)

Saves as both PDF and PNG in output_dir. Uses Okabe-Ito colorblind-friendly palette. DPI=300 for PNG.