From 5b2e9f07a757a8adb855d4cfdad2771c8e732325 Mon Sep 17 00:00:00 2001
From: 13acts <134930647+13acts@users.noreply.github.com>
Date: Mon, 4 Aug 2025 11:54:50 +0700
Subject: [PATCH] fix enrichment

Cover case where slide does not contain all available id_key in adata object
---
 scniche/analysis/_utils.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/scniche/analysis/_utils.py b/scniche/analysis/_utils.py
index ecb594a..e02a322 100644
--- a/scniche/analysis/_utils.py
+++ b/scniche/analysis/_utils.py
@@ -20,7 +20,11 @@ def enrichment(adata: AnnData, id_key: str, val_key: str, library_key: Optional[
         obs[library_key] = 1
     library_list = sorted(list(set(obs[library_key])))
 
-    df = obs.groupby([library_key, id_key, val_key]).size().unstack().fillna(0)
+    df = pd.crosstab(
+        index=[obs[library_key], obs[id_key]],
+        columns=obs[val_key],
+        dropna=False
+    )
     df_list = []
     for i in library_list:
         df_tmp = df.loc[(i,)]