import scanpy as sc
import matplotlib.pyplot as plt
[docs]
def plot_root_cell(adata, color=None, basis='umap', **kwargs):
if 'ot_ct_root' in adata.uns.keys():
fig, axes = plt.subplots(1,2, **kwargs)
root = adata.uns['ot_root']
sc.pl.embedding(adata, basis=basis, show=False, color=color, ax=axes[0], legend_loc='on data', title='OT root cell')
axes[0].scatter(adata.obsm['X_'+basis][root,0], adata.obsm['X_'+basis][root,1], color='red', marker='*', s=200, label='root cell')
root = adata.uns['ot_ct_root']
sc.pl.embedding(adata, basis=basis, show=False, color=color, ax=axes[1], legend_loc='on data', title='OT + CytoTrace(alpha:{}) root cell'.format(adata.uns['cytotrace_alpha']))
axes[1].scatter(adata.obsm['X_'+basis][root,0], adata.obsm['X_'+basis][root,1], color='red', marker='*', s=200)
else:
fig, ax = plt.subplots(1,1, **kwargs)
root = adata.uns['ot_root']
sc.pl.embedding(adata, basis=basis, show=False, color=color, ax=ax, legend_loc='on data', title='OT root cell')
ax.scatter(adata.obsm['X_'+basis][root,0], adata.obsm['X_'+basis][root,1], color='red', marker='*', s=200, label='root cell')