Add number of cells metric (#112)

Author: LouisK92

src/metrics/quality/config.vsh.yaml

@@ -25,6 +25,15 @@ info:
       min: 0
       max: 1
       maximize: true
+    - name: number_of_cells
+      label: Number of Cells
+      summary: "The number of cells in the spatial dataset."
+      description: |
+        The number of cells in the spatial dataset.
+      references:
+        doi: "10.1101/2023.02.13.528102"
+      min: 0
+      maximize: true
 
 resources:
   - type: python_script

src/metrics/quality/script.py

@@ -23,6 +23,7 @@
 metrics = {
     "proportion_of_assigned_reads": proportion_of_assigned_reads(sdata)[0],
     "proportion_of_annotated_cells": proportion_of_annotated_cells(sdata),
+    "number_of_cells": sdata['counts'].n_obs,
 }
 
 print("Write output AnnData to file", flush=True)