PR for data loading in various chapters (theislab#240)

* change data loading in doublet detection

* change dataloading in dim red

* change data loading in doublet detection

* change data loading in quality control

* adjust data loading in normalization

* add pooch to yml

* adjust data loading in annotation

* adjust dataloading in batch correction

* run pre-commit

* change loading in differential expression chapter

jupyter-book/conditions/differential_gene_expression.ipynb

@@ -107,12 +107,17 @@
    },
    "outputs": [
     {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "During startup - Warning message:\n",
-      "Setting LC_CTYPE failed, using \"C\" \n"
-     ]
+     "data": {
+      "text/html": [
+       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"><span style=\"color: #808000; text-decoration-color: #808000; font-weight: bold\">To use sccoda or tasccoda please install ete3 with </span><span style=\"color: #008000; text-decoration-color: #008000; font-weight: bold\">pip install ete3</span>\n",
+       "</pre>\n"
+      ],
+      "text/plain": [
+       "\u001b[1;33mTo use sccoda or tasccoda please install ete3 with \u001b[0m\u001b[1;32mpip install ete3\u001b[0m\n"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
     }
    ],
    "source": [
@@ -127,6 +132,7 @@
     "import numpy as np\n",
     "import random\n",
     "import sc_toolbox\n",
+    "import pertpy \n",
     "\n",
     "import rpy2.rinterface_lib.callbacks\n",
     "import anndata2ri\n",
@@ -212,7 +218,7 @@
     }
    ],
    "source": [
-    "adata = sc.read(\"kang.h5ad\")\n",
+    "adata = pertpy.data.kang_2018()\n",
     "adata"
    ]
   },
@@ -227,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "2ff79170",
+   "id": "b36136e7-0afb-4f32-bb0e-5985103a0d97",
    "metadata": {},
    "outputs": [
     {
@@ -1397,8 +1403,7 @@
    "id": "84f7e880",
    "metadata": {
     "id": "84f7e880",
-    "outputId": "275aba74-3ac8-40ef-b9fb-e378557e3671",
-    "scrolled": false
+    "outputId": "275aba74-3ac8-40ef-b9fb-e378557e3671"
    },
    "outputs": [
     {
@@ -2386,8 +2391,7 @@
    "id": "fcab0310",
    "metadata": {
     "id": "fcab0310",
-    "outputId": "b7e02d5f-26bf-490d-e01c-7cc23d9637d5",
-    "scrolled": false
+    "outputId": "b7e02d5f-26bf-490d-e01c-7cc23d9637d5"
    },
    "outputs": [
     {
@@ -2502,7 +2506,7 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -2516,7 +2520,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16 (main, Dec  7 2022, 01:11:51) \n[GCC 9.4.0]"
+   "version": "3.9.15"
   },
   "vscode": {
    "interpreter": {

jupyter-book/conditions/differential_gene_expression.yml

@@ -17,3 +17,4 @@ dependencies:
   - conda-forge::pip
   - pip:
       - sc-toolbox
+      - pertpy==0.5.0