omicverse.pl.embedding_multi

omicverse.pl.embedding_multi(data, basis, color=None, use_raw=None, layer=None, **kwargs)[source]

Create embedding scatter plots for multi-modal data (MuData) or single-cell data.

Produces scatter plots on specified embeddings, supporting cross-modality feature visualization. For modality-specific embeddings, use format ‘modality:embedding’ (e.g., ‘rna:X_pca’).

Parameters:

  • data – AnnData or MuData object containing embedding and feature data

  • basis (str) – Name of embedding in obsm (e.g., ‘X_umap’) or modality-specific (‘rna:X_pca’)

  • color (Union[str, Sequence[str], None] (default: None)) – Gene names or obs columns to color points by (None)

  • use_raw (Optional[bool] (default: None)) – Whether to use .raw attribute for features (None, auto-determined)

  • layer (Optional[str] (default: None)) – Specific data layer to use for coloring (None)

  • **kwargs – Additional arguments passed to embedding plotting function

Returns:

Plot axes or figure depending on underlying plotting function