Creating a plot of number cells vs UMI count

Hello all,

I am trying to construct a plot which plots the number of cells on the x axis and the UMI count on Y axis, with features/genes being the data points. How can I achieve this in ScanPy?

Thank you for all the help!


Is that the so-called knee plot?

A friend suggested ordering the cells on the x-axis by biggest to smallest (n_counts), then log counts on y axis

Maybe you want to do something like this?

import scanpy as sc
import seaborn as sns

sc.pp.calculate_qc_metrics(adata, inplace=True)

sns.jointplot(adata.obs, "log1p_n_genes_by_counts", "log1p_total_counts")