From a89d2fa2ab5fd9394e2c0fd9b39435945c7439e0 Mon Sep 17 00:00:00 2001
From: caokai1073 <caokai@amss.ac.cn3>
Date: Tue, 28 Jun 2022 09:33:12 +0800
Subject: [PATCH] update

---
 docs/source/examples/.DS_Store                | Bin 6148 -> 6148 bytes
 .../examples/PBMC/pbmc_integration.ipynb      |  40 +++++++++++++++---
 2 files changed, 35 insertions(+), 5 deletions(-)

diff --git a/docs/source/examples/.DS_Store b/docs/source/examples/.DS_Store
index 63902559431d51a924e5c69be8f79cf3f8304032..d3ed87fcbe3c805a65537f0fbf3a98b0e3bff965 100644
GIT binary patch
delta 83
zcmZoMXfc=|#>B)qu~2NHo}wrl0|Nsi1A_nqLj{8#LlHwULy2e3#=_-{jBJ~eSe7zx
jYzSl8%+A5j0o1ZtkmEb^WPTAx4xlEGE|$#^B5Rld@R1RX

delta 144
zcmZoMXfc=|#>B!ku~2NHo}wr_0|Nsi1A_nqLq0<uLn1>CLp($7=7-G7ne{<Z(hMmK
znLy!mWN9F~l%bd*6{xhBp#Z2Q6$tYtZ(x?@{Rz~g_a6)x7&h}TEoI)!&cV+Cv=3<J
Xcjn3bB90tD>zIJb7&b?UtYHQK4MZY4

diff --git a/docs/source/examples/PBMC/pbmc_integration.ipynb b/docs/source/examples/PBMC/pbmc_integration.ipynb
index 3f24a50..d289bc6 100644
--- a/docs/source/examples/PBMC/pbmc_integration.ipynb
+++ b/docs/source/examples/PBMC/pbmc_integration.ipynb
@@ -382,7 +382,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Epochs: 100%|█████████████████████████████████| 345/345 [14:19<00:00,  2.49s/it, recloss=1143.28,klloss=12.49,otloss=5.70]\n"
+      "Epochs: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 345/345 [14:24<00:00,  2.51s/it, recloss=1143.28,klloss=12.49,otloss=5.70]\n"
      ]
     }
    ],
@@ -453,6 +453,36 @@
     "sc.pl.umap(adata, color=['source', 'cell_type'])"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "de71e6ba",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "F1: 0.7776889599431566\n",
+      "ARI: 0.6321860186421134\n",
+      "NMI: 0.6718827954523922\n",
+      "Batch Entropy: 0.5858338812322246\n",
+      "Silhouette: 0.5916472971439362\n"
+     ]
+    }
+   ],
+   "source": [
+    "adata1 = adata[adata.obs['domain_id']=='0']\n",
+    "adata2 = adata[adata.obs['domain_id']=='1']\n",
+    "y_test = up.metrics.label_transfer(adata2, adata1, label='cell_type', rep='X_umap')\n",
+    "from sklearn.metrics import adjusted_rand_score, normalized_mutual_info_score, f1_score\n",
+    "print('F1:', f1_score(adata1.obs['cell_type'], y_test, average='micro'))\n",
+    "print('ARI:', adjusted_rand_score(adata1.obs['cell_type'], y_test))\n",
+    "print('NMI:', normalized_mutual_info_score(adata1.obs['cell_type'], y_test))\n",
+    "print('Batch Entropy:', up.metrics.batch_entropy_mixing_score(adata.obsm['X_umap'], adata.obs['domain_id']))\n",
+    "print('Silhouette:', up.metrics.silhouette(adata.obsm['X_umap'], adata.obs['cell_type']))"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "7f23a7ea",
@@ -464,7 +494,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "id": "d6c480b2",
    "metadata": {},
    "outputs": [],
@@ -474,7 +504,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "id": "5561c6b3",
    "metadata": {},
    "outputs": [
@@ -519,7 +549,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "id": "5eb7b985",
    "metadata": {},
    "outputs": [
@@ -591,7 +621,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "id": "b5851da3",
    "metadata": {},
    "outputs": [