SC2Spa.pl.DrawCT3

SC2Spa.pl.DrawCT3(adata: AnnData, CT_list: list, coords_name='spatial_mapping', s=3, FM=True, scST=False, c_name='cell_type_med_resolution', legend=False, root='Transfer1/FM_Valid3/', figsize=(10, 10), save=None)

Display original locations or predicted locations of beads/cells of selected types. Beads/cells are colored according to anatomy/cell type. A figure will be saved to root+save+’.png’ The legend of the figure will be saved to root + save + ‘_legend.png’

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_list

A list that contains the cell types to be shown. The cell types must be in adata.obs[c_name]

c_name

Name of cell type column in adata.obs

s

size of beads in the figure

legend

Draw legend in the figure if True

Returns

None