SC2Spa.pl.DrawSVG

SC2Spa.pl.DrawSVG(adata: ~anndata._core.anndata.AnnData, GeneList: ~pandas.core.frame.DataFrame, target_field: str, coords_name='spatial', n_genes=9, s=2, lim=False, alpha=0.8, xlim=[650, 5750], ylim=[650, 5750], cmap=<matplotlib.colors.ListedColormap object>, FM=True, scST=False, root='figures/SVG/', fontsize=40, CT_name='MCT', CT='', Sparse=True, Bottom=False, output=None)

Show the expression of location predictive genes (or spatially variable genes)

in all cells or one cell type

The integrated figure will be saved as root + output + ‘.png’ if output!=None The sub-figures will be saved as root + Genes[i] + ‘_’ + CT + ‘.png’

Parameters

adata

anndata file. Cell type information should be stored in adata.obs[CT_name] if CT!=’’ 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 name to be drawn. Default ‘’.

GeneList

A DataFrame that stores spatial variance information in target_field column

target_field

The column that stores spatial variance information in GeneList

n_genes

number of genes to be drawn

alpha

Transparency score of beads. 1 is completely opaque. 0 is completely transparent.

s

size of beads in the figure

FM

Draw finely mapped beads of cells if True

scST

Draw reconstructed single-cell ST data if True

cmap

colormap. See matplotlib

fontsize

font size of title

Sparse

True if the gene expression matrix is saved in sparse format

Bottom

Prioritize in ascending order if True

Returns

None