Add CC to QC overview plots in PCA or UMAP
# Visualize cells in PCA
# plots
colors_to_plot=['total_counts', metacol, 'n_genes_by_counts', 'pct_counts_is_mito','pct_counts_is_ribo']
label_to_plot =['total_counts', metacol, 'n_genes_by_counts', 'pct_counts_mito','Mitochondrial content']
#if phases given add them to plot
if any(adata.obs.columns.isin(['phase'])):
colors_to_plot = colors_to_plot + ['phase']
label_to_plot = label_to_plot + ['CC-phase']
# Show PCA for Cell cycle and other values
scanpy.pl.pca(adata,color = colors_to_plot,ncols=3,title=label_to_plot, legend_loc = 'right margin')
plt.tight_layout()
plt.savefig(fname=local_path+figures+"02-1-PCA-with-cell_cycle.pdf")
Edited by Hendrik Schultheis