Overlay paga-trajectory result on umap

[parkjooyoung99]

I know there is a function 'sc.pl.paga_compare' but i wonder if i can overlay paga-trajectory result on umap.

Thank you!

[shaln]

@parkjooyoung99 This is the code I used to first re-orient the PAGA plot to mimic the UMAP.

# Compare UMAP and PAGA layouts
fig,axs=plt.subplots(1,2,figsize=(20,10), dpi=250)
sc.pl.umap(control_sce, color='subclusters', ax=axs[0], show=False, size=30, legend_loc='on data',
           legend_fontsize=15, legend_fontoutline=5, frameon=False, title='UMAP')
sc.pl.paga(control_sce,ax=axs[1], frameon=False, title='PAGA (Threshold = 0)', 
           node_size_scale=10, edge_width_scale=3, fontsize=15, fontoutline=5,
           threshold=0, save='_umap-compare_thr0.png')

Then I used this next chunk of code to overlap the PAGA onto the UMAP. Hope this helps :)

# Define PAGA positions based on the UMAP layout -
# for each cluster we use the mean of the UMAP positions from the cells in that cluster
pos=pd.DataFrame(control_sce.obsm['X_umap'],index=control_sce.obs_names)
pos['group']=control_sce.obs[control_sce.uns['paga']['groups']]
pos=pos.groupby('group').mean()

# Plot UMAP in the background
ax=sc.pl.umap(control_sce,show=False, size=30, legend_loc='bottom',
              legend_fontsize=15, legend_fontoutline=5, frameon=False, title='UMAP')
# Plot PAGA ontop of the UMAP
sc.pl.paga(control_sce, frameon=False, title='PAGA (Threshold = 0)', threshold=0, 
           node_size_scale=6, edge_width_scale=3, fontsize=12, fontoutline=5, 
           pos=pos.values, random_state=0, ax=ax, save='_umap-overlay_thr0.png')