From 29a8deda369b932a93687e7204500ccfdefa59a9 Mon Sep 17 00:00:00 2001
From: alex-l-kong <alkong@ucdavis.edu>
Date: Thu, 29 Aug 2024 13:48:30 -0700
Subject: [PATCH] Make channel ordering consistent in Pixie pipeline

---
 templates/2_Pixie_Cluster_Pixels.ipynb | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/templates/2_Pixie_Cluster_Pixels.ipynb b/templates/2_Pixie_Cluster_Pixels.ipynb
index cac7f3a6b..00b9770b0 100644
--- a/templates/2_Pixie_Cluster_Pixels.ipynb
+++ b/templates/2_Pixie_Cluster_Pixels.ipynb
@@ -336,7 +336,10 @@
     "            \"CD163_nuc_exclude\", \"CK17\", \"Collagen1\", \"Fibronectin\", \n",
     "            \"ECAD_smoothed\", \"HLADR\", \"SMA\", \"Vim\"]\n",
     "blur_factor = 2\n",
-    "subset_proportion = 0.1"
+    "subset_proportion = 0.1\n",
+    "\n",
+    "# ensures consistent ordering of channel names across files\n",
+    "channels = sorted(channels)"
    ]
   },
   {
@@ -928,7 +931,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.10.14"
   },
   "nbdime-conflicts": {
    "local_diff": [