scalex.plot.embedding

scalex.plot.embedding(adata, color='celltype', color_map=None, groupby='batch', groups=None, cond2=None, v2=None, save=None, legend_loc='right margin', legend_fontsize=None, legend_fontweight='bold', sep='_', basis='X_umap', size=10, show=True)

plot separated embeddings with others as background

Parameters:

• adata – AnnData

• color – meta information to be shown

• color_map – specific color map

• groupby – condition which is based-on to separate

• groups – specific groups to be shown

• cond2 – another targeted condition

• v2 – another targeted values of another condition

• basis – embeddings used to visualize, default is X_umap for UMAP

• size – dot size on the embedding