update docs

Author: lzj1769

docs/tutorials/index.rst

@@ -8,3 +8,4 @@ We provide several tutorials to help you get started with Cell2Net and explore i
 
    k562/index
    pbmc/index
+   misc/index

docs/tutorials/misc/01_create_mudata.ipynb

@@ -0,0 +1,73 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f08e5563",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31mRunning cells with 'zl_cell2net (Python 3.12.13)' requires the ipykernel package.\n",
+      "\u001b[1;31m<a href='command:jupyter.createPythonEnvAndSelectController'>Create a Python Environment</a> with the required packages.\n",
+      "\u001b[1;31mOr install 'ipykernel' using the command: 'conda install -n zl_cell2net ipykernel --update-deps --force-reinstall'"
+     ]
+    }
+   ],
+   "source": [
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")\n",
+    "\n",
+    "import mudata as md\n",
+    "import muon as mu\n",
+    "import scanpy as sc\n",
+    "\n",
+    "md.set_options(pull_on_update=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0e27c8ff",
+   "metadata": {},
+   "source": [
+    "# in this tutorial, we show how to create mudata from 10x multiome output file\n",
+    "\n",
+    "# data is downloaded from [here](https://www.10xgenomics.com/datasets/human-kidney-cancer-nuclei-isolated-with-chromium-nuclei-isolation-kit-saltyez-protocol-and-10x-complex-tissue-dp-ct-sorted-and-ct-unsorted-1-standard)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2caed670",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mu.read"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "zl_cell2net",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/tutorials/misc/index.rst

@@ -0,0 +1,9 @@
+Miscellaneous
+=============================
+
+Miscellaneous tutorials related to Cell2Net.
+
+.. toctree::
+   :maxdepth: 1
+
+   01_create_mudata

docs/tutorials/pbmc/01_pretrain.ipynb

@@ -566,7 +566,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": null,
    "id": "c47e999a",
    "metadata": {},
    "outputs": [
@@ -665,7 +665,7 @@
     }
    ],
    "source": [
-    "model.train(df_train=df_train, df_valid=df_valid, max_epochs=100, \n",
+    "model.train(df_train=df_train, df_valid=df_valid, max_epochs=100,\n",
     "            batch_size=512, weight_decay=1e-04, lr=3e-04)"
    ]
   },
@@ -764,7 +764,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": null,
    "id": "77e2dc0a",
    "metadata": {},
    "outputs": [
@@ -798,7 +798,7 @@
     "# set axis-x and axis-y the same scale\n",
     "plt.xlim(_min, _max)\n",
     "plt.ylim(_min, _max)\n",
-    "plt.title('pearsonR = {:.3f}'.format(pearsonR))\n",
+    "plt.title(f'pearsonR = {pearsonR:.3f}')\n",
     "plt.xlabel('True Accessibility (log1p counts)')\n",
     "plt.ylabel('Predicted Accessibility (log1p counts)')\n",
     "plt.tight_layout()"
@@ -818,7 +818,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": null,
    "id": "6bb36af8",
    "metadata": {},
    "outputs": [
@@ -853,7 +853,7 @@
     "# set axis-x and axis-y the same scale\n",
     "plt.xlim(_min, _max)\n",
     "plt.ylim(_min, _max)\n",
-    "plt.title('pearsonR = {:.3f}'.format(pearsonR))\n",
+    "plt.title(f'pearsonR = {pearsonR:.3f}')\n",
     "plt.gca().set_aspect('equal', adjustable='box')\n",
     "plt.xlabel('True Accessibility (log1p counts)')\n",
     "plt.ylabel('Predicted Accessibility (log1p counts)')\n",
@@ -904,7 +904,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "zl_cell2net",
+   "display_name": "zl_src",
    "language": "python",
    "name": "python3"
   },
@@ -918,7 +918,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,