troutpy.pl.gene_communication

troutpy.pl.gene_communication#

troutpy.pl.gene_communication(sdata, kind='heatmap', gene='', celltype_key='cell type', vmax=None, vmin=None, cmap='BuPu', dendrogram_ratio=0.1, **kwargs)#

Plot gene-level cell type-cell type interaction strength as a heatmap or chord diagram.

Parameters:

  • sdata (SpatialData) – The spatial data object containing interaction scores.

  • kind (str (default: 'heatmap')) – Type of plot, either "heatmap" or "chord".

  • gene (str (default: '')) – Name of the gene to plot. Must be present in sdata["source_score"].uns["gene_interaction_names"].

  • celltype_key (str (default: 'cell type')) – Key for cell type colors in sdata["table"].uns.

  • vmax (Optional[float] (default: None)) – Max value for colormap scaling.

  • vmin (Optional[float] (default: None)) – Min value for colormap scaling.

  • cmap (str (default: 'BuPu')) – Colormap for heatmap or chord diagram.

  • dendrogram_ratio (float (default: 0.1)) – Passed to seaborn.clustermap().

  • kwargs – Additional arguments passed to seaborn.clustermap() or mpl_chord_diagram.chord_diagram().

Return type:

None

Returns:

None

Contents