SC2Spa.pl.DrawCT1

SC2Spa.pl.DrawCT1(adata: AnnData, CT: str, ax=None, coords_name='spatial', s=2, FM=True, scST=False, c_name='leiden', root='transfer2/FM_Valid2/', figsize=(10, 10), save=None)

Show the spatial locations of a type of cells or beads

The figure will be saved as root + save + ‘_’ + CT + ‘.png’ if save!=None

Parameters

adata

anndata file. Cell type information should be stored in adata.obs[c_name] Fine mapping result should be stored in `adata.obs[‘FM’] if FM==True Coordinate Information should be stored in adata.obsm[coords_name] Reconstruction info should be stored in adata.obs[‘Recon_scST’]

CT

The cell type to be drawn. it must be one category in adata.obs[c_name]

ax

matplotlib ax where the figure is plotted

coords_name

Coordinate Information should be stored in adata.obsm[coords_name]

s

size of beads in the figure

FM

Draw finely mapped beads or cells if True.

scST

Draw reconstructed single-cell ST data if True.

figsize

figure size

Returns

None