fixed tutorial

tutorials/tutorial.ipynb

@@ -11,7 +11,6 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "from scipy.spatial.transform import Rotation\n",
-    "import umap\n",
     "\n",
     "from cryo_sbi import CryoEmSimulator\n",
     "import cryo_sbi.inference.train_npe_model as train_npe_model\n",
@@ -20,6 +19,24 @@
     "from cryo_sbi.utils.visualize_models import plot_model"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### If you want to run the latent space analysis with UMAP, you need to install the following package:\n",
+    "You can find the installation instructions [here](https://umap-learn.readthedocs.io/en/latest/). \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# If you installed umap you can import it here \n",
+    "import umap"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -363,7 +380,7 @@
     "plt.scatter(\n",
     "    latent_vecs_transformed[:, 0],\n",
     "    latent_vecs_transformed[:, 1],\n",
-    "    c=dist,\n",
+    "    c=side_length,\n",
     "    cmap=\"viridis\",\n",
     "    s=10,\n",
     ")\n",
@@ -389,13 +406,6 @@
     "plt.xlabel(\"UMAP 1\")\n",
     "plt.ylabel(\"UMAP 2\")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {