spapros.pl.clf_genes_umaps

spapros.pl.clf_genes_umaps(adata, df, basis='X_umap', ct_key='celltype', n_cols=4, size_factor=1, fontsize=18, show=True, save=None)

Plot umaps of genes needed for cell type classification of each cell type.

Parameters:

• adata (AnnData) – AnnData with ct_key in adata.obs and basis in adata.obsm.

• df (DataFrame) –

  Dataframe with genes as index and the following columns:

  • ’decision_celltypes’: List of celltypes for which the gene is needed for classification.

  • ’rank’: Forest classification rank of the gene.

  • ’importance_score’: Importance score of the gene.

  Optional columns: TODO: do we need to list them here?

  • ’marker_celltypes’: List of celltypes for which the gene is a marker according to the known marker

    list. TODO: check if also DE “markers” alowed?

  • ’decision_title’: Subplot title.

  • ’marker_title’: Subplot title used if gene is marker. TODO: why decision_title AND marker_title?

  • ’decision_cmap’: Matplotlib colormap.

  • ’marker_cmap’: Matplotlib colormap used if gene is marker. TODO: why decision_cmap and marker_cmap (and why cmap at all…)

• basis (str) – Name of the obsm embedding to use.

• ct_key (str) – Column name in adata.obs where celltypes are stored.

• n_cols (int) – Number of subplot columns.

• fontsize (int) – Matplotlib fontsize.

• size_factor (float) – Scale factor for figure width and height.

• show (bool) – Whether to display the plot.

• save (Optional[str]) – Save the plot to path.

Returns:

Figure can be shown (default True) and stored to path (default None). Change this with show and save.

Return type:

None