HoloNet.plotting.select_w

HoloNet.plotting.select_w(adata, w_best, size=1.4, alpha=0.7, cmap='Spectral_r', data_type='Visium', fname=None, **kwargs)

Plot the covering spatial region of ligands derived from one spot.

Parameters

adata AnnData

Annotated data matrix.

w_best float

A distance parameter in edge weighting function controlling the covering region of ligands. ‘default_w_visium’ function provides a recommended value of w_best.

size float (default: 1.4)

The size of each spot, see sc.pl.spatial in Scanpy.

alpha float (default: 0.7)

The alpha value of each spot.

cmap Colormap | strUnion[Colormap, str] (default: 'Spectral_r')

The color map of feature value of each spot, defaultly as ‘Spectral_r’

data_type str (default: 'Visium')

Select in Visium or SeqFISH

fname str | Path | NoneUnion[str, Path, None] (default: None)

The output file name. If None, not save the figure. Note that not add path name, sc.pl.spatial will add ‘show’ before the file name.

kwargs

Other parameters in scanpy.pl.spatial or scanpy.pl.embedding.