I'm trying to find if there is any insight into sequence depth (x-axis) vs. expression level (y-axis) from a single-cell RNA data and create a scatter plot.
I'm using scanpy tool to do the downstream analysis of the scRNA analysis.
To achieve what I'm trying to attempt the sequence depth part I think will be total_counts so adata.obs['total_counts'] to extract/parse for that particular information however I'm a bit lost/confused on how to calculate expression level not sure if that will be 'n_genes_by_counts' or if I have to use a separate, as in manually calculate expression level...
I know that I can create expression level plots for each cluster group or differentially expressed gene but that is not what I am looking for.
Any help is much appreciated and thank you.
