Garfield.plot.niches_enrichment_dotplot

Garfield.plot.niches_enrichment_dotplot(enrichments, niche, type='gsea', figsize=(10, 5), n_enrichments=10, title='auto', cmap=None, qval_cutoff=0.05)[source]

Create a dotplot for the enrichment results (either from Enrichr or GSEA).

Parameters:

  • enrichments (dict) – Dictionary of enrichment results where the key is the niche name and the value is a dataframe of enrichment results.

  • niche (str) – The niche (cluster) to visualize enrichment for.

  • type (str, optional) – The type of enrichment analysis (‘enrichr’ or ‘gsea’). Default is ‘gsea’.

  • figsize (tuple, optional) – Figure size for the plot.

  • n_enrichments (int, optional) – Number of top enrichment terms to display (default is 10).

  • title (str, optional) – Title of the plot (default is ‘auto’, which uses the first gene set’s name).

  • cmap (matplotlib.colors.Colormap, optional) – Colormap for the plot.

  • qval_cutoff (float, optional) – Adjusted p-value or FDR cutoff to filter enrichment terms (default is 0.05).

Returns:

ax – The matplotlib axis containing the plot.

Return type:

matplotlib.axes.Axes