bento.pl.colocation

bento.pl.colocation(sdata, rank, n_top=[None, None, 5], z_score=[False, True, True], cut=None, show_labels=[True, False, True], cluster=[False, True, False], self_pairs=False, figsize=(8, 6), fname=None)

Plot colocation of signatures for specified rank across each dimension.

Parameters:

  • sdata (spatialdata.SpatialData) – Spatial formatted SpatialData

  • rank (int) – Rank of signatures to plot

  • n_top (int, optional) – Number of top features to plot, by default 10

  • z_score (bool, optional) – Whether to z-score each column of the matrix, by default False

  • cut (float, optional) – Max cut-off for z-score color mapping, by default None

  • show_labels (list, optional) – Whether to show labels for each dimension, by default [True, False, False]

  • cluster (list, optional) – Whether to cluster rows, by default [False, True, True]

  • self_pairs ([True, False, “only”], optional) – Whether to include self-pairs, value “only” shows only self-pairs, by default True

  • fname (str, optional) – Path to save figure, by default None