update

+ modified requirements + minor function changes + minor adaptions of notebooks (remove paths)
menchelab · Mar 18, 2022 · 6f1eb15 · 6f1eb15
1 parent a31e7e8
commit 6f1eb15
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Showing 5 changed files with 73 additions and 47 deletions.
diff --git a/Requirements.txt b/Requirements.txt
@@ -8,7 +8,8 @@ colormath==3.0.0
 umap-learn==0.5.0
 pandas==1.3.1
 numpy==1.19.2
-biopython==0.7.4
+bio==0.7.4
+biopython==1.79
 html2image==2.0.1
 python_igraph==0.9.6
 scikit_learn==0.24.2

diff --git a/cartoGRAPHs_AQuickStarter.ipynb b/cartoGRAPHs_AQuickStarter.ipynb
@@ -37,14 +37,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 4,
    "id": "blocked-journalism",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "G = nx.scale_free_graph(n=1000)"
+    "G = nx.scale_free_graph(n=100)"
    ]
   },
   {
@@ -57,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 10,
    "id": "f7dac009-f8cc-4705-8608-22eee785e233",
    "metadata": {},
    "outputs": [],
@@ -95,7 +95,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 11,
    "id": "4df461bd-874e-403b-9b79-d227439804d6",
    "metadata": {},
    "outputs": [],
@@ -155,7 +155,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 12,
    "id": "respective-plumbing",
    "metadata": {
     "tags": []
@@ -195,7 +195,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 13,
    "id": "noted-thompson",
    "metadata": {},
    "outputs": [],
@@ -222,6 +222,14 @@
     "                colors = None\n",
     "               )"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f7068290-7cdf-4d2b-ad04-4c44651f9b85",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/cartoGRAPHs_ExemplaryNotebook.ipynb b/cartoGRAPHs_ExemplaryNotebook.ipynb
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "fc201309-484c-475d-9c9e-85f35a74b6fc",
    "metadata": {},
    "outputs": [],
@@ -48,14 +48,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "blocked-journalism",
    "metadata": {
     "tags": []
    },
    "outputs": [],
    "source": [
-    "G = nx.scale_free_graph(n=1000)\n",
+    "G = nx.scale_free_graph(n=100)\n",
     "\n",
     "l_nodefeatures = ['nodeID:'+str(i) for i in list(G.nodes())]\n",
     "d_nodefeatures = dict(zip(G.nodes(),l_nodefeatures))\n",
@@ -93,7 +93,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 6,
    "id": "f7dac009-f8cc-4705-8608-22eee785e233",
    "metadata": {},
    "outputs": [],
@@ -153,10 +153,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "id": "560d27d0-698f-4509-802a-64a56f084f73",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/chris/opt/anaconda3/lib/python3.8/site-packages/umap/umap_.py:125: UserWarning: A few of your vertices were disconnected from the manifold.  This shouldn't cause problems.\n",
+      "Disconnection_distance = 1 has removed 6730 edges.\n",
+      "It has only fully disconnected 1 vertices.\n",
+      "Use umap.utils.disconnected_vertices() to identify them.\n",
+      "  warn(\n",
+      "/Users/chris/opt/anaconda3/lib/python3.8/site-packages/umap/umap_.py:125: UserWarning: A few of your vertices were disconnected from the manifold.  This shouldn't cause problems.\n",
+      "Disconnection_distance = 1 has removed 6730 edges.\n",
+      "It has only fully disconnected 1 vertices.\n",
+      "Use umap.utils.disconnected_vertices() to identify them.\n",
+      "  warn(\n"
+     ]
+    }
+   ],
    "source": [
     "posG2D = generate_layout(G, \n",
     "                        dim = 2, \n",
@@ -187,7 +204,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 9,
    "id": "0ae5605c-bf2c-409a-b207-e479e2979de3",
    "metadata": {},
    "outputs": [],
@@ -207,16 +224,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 10,
    "id": "fbf90b22-ed6b-4b7d-9b33-4364ffd1f1ee",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 1min 30s, sys: 8.45 s, total: 1min 38s\n",
-      "Wall time: 1min 4s\n"
+      "CPU times: user 1min 21s, sys: 8.21 s, total: 1min 29s\n",
+      "Wall time: 53.5 s\n"
      ]
     }
    ],
@@ -234,16 +251,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 11,
    "id": "de619bd2-17b9-4a86-940c-f32ed8d0f85a",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 1min 52s, sys: 7.22 s, total: 1min 59s\n",
-      "Wall time: 47.1 s\n"
+      "CPU times: user 1min 13s, sys: 4.44 s, total: 1min 17s\n",
+      "Wall time: 33 s\n"
      ]
     }
    ],
@@ -283,12 +300,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 16,
    "id": "liked-newfoundland",
    "metadata": {},
    "outputs": [],
    "source": [
-    "scale_factor = 2\n",
+    "scale_factor = 0.5\n",
     "nodesize = list(draw_node_degree(G, scale_factor).values())\n",
     "d_nodesize = dict(draw_node_degree(G, scale_factor))"
    ]
@@ -316,7 +333,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 13,
    "id": "df9d820e-9fb6-44f5-8441-6e836d0fa8e7",
    "metadata": {},
    "outputs": [],
@@ -389,17 +406,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 17,
    "id": "4df461bd-874e-403b-9b79-d227439804d6",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'output_plots/2Dlayouts/2Dportrait_global.html'"
+       "'2Dportrait_precalculated.html'"
       ]
      },
-     "execution_count": 34,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -410,10 +427,10 @@
     "              d_colors = d_nodecolors, \n",
     "              d_size = d_nodesize, \n",
     "              d_legend = d_nodelegend,\n",
-    "              path = 'output_plots/2Dlayouts/', \n",
+    "              path = '', \n",
     "              fname = '2Dportrait'+'_'+layout_method, \n",
     "              scheme = 'light',\n",
-    "              #with_edges = False\n",
+    "              with_edges = False\n",
     "             )"
    ]
   },
@@ -434,7 +451,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "export_to_csv2D(path = 'output_plots/VRlayouts/', \n",
+    "export_to_csv2D(path = '', \n",
     "                layout_namespace = '2Dportrait'+'_'+layout_method, \n",
     "                posG2D, \n",
     "                nodecolors)"
@@ -452,17 +469,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 18,
    "id": "81114f28-9d9d-4157-9ead-6d252d42f956",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'output_plots/3Dlayouts/3Dportrait_global.html'"
+       "'3Dportrait_precalculated.html'"
       ]
      },
-     "execution_count": 33,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -473,10 +490,10 @@
     "              d_colors = d_nodecolors, \n",
     "              d_size = d_nodesize, \n",
     "              d_legend = d_nodelegend,\n",
-    "              path = 'output_plots/3Dlayouts/', \n",
+    "              path = '', \n",
     "              fname = '3Dportrait'+'_'+layout_method, \n",
     "              scheme = 'dark',\n",
-    "              #with_edges = False\n",
+    "              with_edges = False\n",
     "             )"
    ]
   },
@@ -495,7 +512,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "export_to_csv3D(path = 'output_plots/VRlayouts/', \n",
+    "export_to_csv3D(path = '', \n",
     "                layout_namespace = '3Dportrait'+layout_method, \n",
     "                posG3D, \n",
     "                nodecolors)"
@@ -542,7 +559,7 @@
     "              d_colors = d_nodecolors, \n",
     "              d_size = d_nodesize, \n",
     "              d_legend = d_nodelegend,\n",
-    "              path = 'output_plots/3Dlayouts/', \n",
+    "              path = '', \n",
     "              fname = 'Topographic'+layout_method, \n",
     "              scheme = 'light')"
    ]
@@ -562,7 +579,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "export_to_csv3D(path = 'output_plots/VRlayouts/',\n",
+    "export_to_csv3D(path = '',\n",
     "                layout_namespace = 'Topographic'+layout_method, \n",
     "                posG = posG_topographic, \n",
     "                colors = nodecolors)"
@@ -594,7 +611,7 @@
     "              d_colors = d_nodecolors, \n",
     "              d_size = d_nodesize, \n",
     "              d_legend = d_nodelegend, \n",
-    "              path = 'output_plots/3Dlayouts/', \n",
+    "              path = '', \n",
     "              fname = 'Geodesic'+layout_method, \n",
     "              scheme = 'light')"
    ]
@@ -614,7 +631,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "export_to_csv3D(path = 'output_plots/VRlayouts/', \n",
+    "export_to_csv3D(path = '', \n",
     "                layout_namespace = 'Geodesic'+layout_method, \n",
     "                posG = posG_geodesic, \n",
     "                colors = nodecolors)"