scimap.pl.spatial_interaction

Short description

The function allows users to generate a heatmap to visualize spatial interaction output from sm.tl.spatial_interaction. The intensity represents number of interactions (scaled) and blank regions represent non-significant results.

Parameters

adata : AnnData object

spatial_interaction: string (The default is 'spatial_interaction')
In order to locate the spatial_interaction data within the AnnData object please provide the output label/columnname of sm.tl.spatial_interaction function.

summarize_plot : bool, optional (The default is True)
In the event of analyzing multiple images, this argument allows users to plot the average cell-cell interaction across all images.

p_val : float, optional (The default is 0.05.)
P-value cut-off above which interactions are not considered significant.

subset_phenotype : list, optional (The default is None)
If user requires to visualize a subset of phenotypes, it can be passed here. e.g. subset_phenotype = ['celltype_A', 'celltype_B'].

subset_neighbour_phenotype : list, optional (The default is None)
If user requires to visualize a subset of interacting phenotypes, it can be passed here. e.g. subset_neighbour_phenotype = ['celltype_C', 'celltype_D'].

nonsig_color : string, optional (The default is 'grey')
Color for non-significant interactions (Interactions above the P-value cut-off will use this color).

row_cluster : bool, optional (The default is False)
Cluster Rows.

col_cluster : bool, optional (The default is False)
Cluster Columns.

binary_view : bool, optional (The default is False)
Removes the intensity of intreaction and plots significant interactions and avoidance in a binary format.

cmap : string, optional (The default is 'vlag')
Color map to use for continous variables. Can be a name or a Colormap instance (e.g. 'magma', 'viridis').

return_data : bool, optional (The default is False)
When True, return the data used for plotting.

**kwargs: key:value pairs.
Are passed to sns.clustermap. Pass other parameters that works with sns.clustermap. e.g. linecolor='black'

Returns

Heatmap

Example

# spatial_interaction heatmap for a single image
sm.pl.spatial_interaction(adata, summarize_plot=True, row_cluster=True, linewidths=0.75, linecolor='black')

# spatial_interaction heatmap for multiple images
sns.set(font_scale=0.6)
m.pl.spatial_interaction(adata, summarize_plot=False, row_cluster=True, col_cluster=True, yticklabels=True)