Updated data link

fanzhanglab · Jan 25, 2025 · ba7f132 · ba7f132
1 parent d281af9
commit ba7f132
Showing 1 changed file with 2 additions and 34 deletions.
diff --git a/vignettes/test_vignette.ipynb b/vignettes/test_vignette.ipynb
@@ -22,33 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# import pyCellPhenoX\n",
-    "# import pandas as pd"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n"
-     ]
-    }
-   ],
-   "source": [
-    "import sys\n",
-    "sys.path.append('/Users/zhanglab_mac2/Documents/GitHub/pyCellPhenoX')\n",
-    "import pyCellPhenoX.CellPhenoX\n",
-    "import pyCellPhenoX.preprocessing\n",
-    "from pyCellPhenoX.neighborhoodAbundanceMatrix import neighborhoodAbundanceMatrix\n",
-    "import pyCellPhenoX.nonnegativeMatrixFactorization\n",
-    "import pyCellPhenoX.principalComponentAnalysis\n",
-    "import pyCellPhenoX.plot_interpretablescore_boxplot\n",
-    "import pyCellPhenoX.plot_interpretablescore_umap\n",
+    "import pyCellPhenoX\n",
     "import pandas as pd"
    ]
   },
@@ -360,8 +334,7 @@
     }
    ],
    "source": [
-    "# nam_file = \"https://olucdenver-my.sharepoint.com/:x:/g/personal/jade_young_cuanschutz_edu/EZ_TyABgKxVNqJyQlVnWgm8Byj0_5p5vAdwuLrJQbt8W5Q?e=mDoK2t\"\n",
-    "nam_file = \"/Users/zhanglab_mac2/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/Zhang_Lab/Manuscripts/CellPhenoX/Data/UC/NAM_cellXnbhd.csv\"\n",
+    "nam_file = \"https://drive.google.com/file/d/1qHFqHaqJGCbgV8FO34ojiR-mjH7bZiH9/view?usp=sharing\"\n",
     "nam = pd.read_csv(nam_file, index_col=0)\n",
     "nam.head()"
    ]
@@ -560,11 +533,6 @@
     "The function for running this step is `model_training_shap_val`. You can pass the path to a specific output path for the produced plots."
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": 12,