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

  • 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