SC2Spa.pl.Superimpose

SC2Spa.pl.Superimpose(adata: AnnData, coords_name='spatial', G1='APOE', G2='NRGN', s=2, C1='Reds', C2='Blues', figsize=(10, 10), alpha1=0.5, alpha2=0.7, save_root='figures/BME/', save=True)

Show the spatial gene expressions of two genes and their superimposed images

The figures will be saved as if save==True: save_root + G1 + ‘_1.png’ (Spatial Gene Expression of Gene1) save_root + G2 + ‘_1.png’ (Spatial Gene Expression of Gene2) save_root + G1 + ‘_’ + G2 + ‘.png’ (Draw Gene1 first in the superimposed figure) save_root + G2 + ‘_’ + G1 + ‘.png’ (Draw Gene2 first in the superimposed figure)

Parameters

adata

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

G1

name of Gene1

G2

name of Gene2

s

size of beads in the figure. The second gene in the superimposed figures will be drawn in the size of s/4

alpha1

Transparency score of beads of the figures for only one gene.

1 is completely opaque. 0 is completely transparent.

alpha2

Transparency score of beads of the superimposed figures.

1 is completely opaque. 0 is completely transparent.

C1

color (map) for the Gene1

C2

color (map) for the Gene2

Returns

None