omicverse.pl.geneset_wordcloud

class omicverse.pl.geneset_wordcloud(adata, cluster_key, pseudotime, resolution=1000, figsize=(4, 10))

Build cluster-wise gene-set word clouds along pseudotime.

Parameters:

• adata (AnnData) – AnnData containing feature scores (for example pathway activity or gene programs).

• cluster_key (str) – adata.obs key defining cell clusters/groups.

• pseudotime (str) – adata.obs key defining pseudotime ordering.

• resolution (int, optional) – Vertical grid resolution for stacked plotting.

• figsize (tuple, optional) – Figure size for word-cloud visualization.

Returns:

Initializes word-cloud construction settings.

Return type:

None

Examples

>>> gw_obj = ov.utils.geneset_wordcloud(adata=adata_aucs[:, var_name], cluster_key="g1", pseudotime="pt_via")

__init__(adata, cluster_key, pseudotime, resolution=1000, figsize=(4, 10))

Initialize word-cloud builder from AnnData and grouping metadata.

Methods

__init__(adata, cluster_key, pseudotime[, ...])	Initialize word-cloud builder from AnnData and grouping metadata.
get()	Build per-cluster word-cloud objects from dominant features.
get_geneset()	Return the feature-to-cluster assignment table used for word-cloud generation.
get_wordcloud()	Return generated word-cloud objects.
plot()	Plot stacked cluster word clouds ordered by mean pseudotime.
plot_heatmap([n_convolve, figwidth, cmap, ...])	Plot cluster word clouds together with a pseudotime-smoothed heatmap.