Make cell type percent out of total rather than mean, hide unlabeled subject cells from t-SNE

Author: dibidave

capblood_seq_viz/figures/summary.py

@@ -28,7 +28,7 @@ def get_cell_tSNE_figure(group_by=data.Cell_Grouping.SUBJECT):
         cell_coordinates = cell_coordinates_by_group[group_name]
 
         if group_name is None:
-            group_name = "Other"
+            continue
 
         scatter = graph_objects.Scattergl(
             x=cell_coordinates[:, 0],

notebooks/Cell Type Counts.ipynb

@@ -63,7 +63,9 @@
     "            cell_percentage = num_cells/num_subject_cells\n",
     "            cell_type_percentages[cell_type].append(cell_percentage)\n",
     "    cell_type_errors[cell_type] = numpy.std(cell_type_percentages[cell_type])\n",
-    "    cell_type_percentages[cell_type] = numpy.mean(cell_type_percentages[cell_type])\n",
+    "\n",
+    "for cell_type in config.CELL_TYPES:\n",
+    "    cell_type_percentages[cell_type] = cell_type_num_cells[cell_type]/sum(cell_type_num_cells.values())\n",
     "\n",
     "# Repeat for each subtype\n",
     "cell_subtype_percentages = {}\n",
@@ -87,7 +89,7 @@
     "                cell_percentage = num_cells/num_subject_cells\n",
     "                cell_subtype_percentages[cell_type][cell_subtype].append(cell_percentage)\n",
     "        cell_subtype_errors[cell_type][cell_subtype] = numpy.std(cell_subtype_percentages[cell_type][cell_subtype])\n",
-    "        cell_subtype_percentages[cell_type][cell_subtype] = numpy.mean(cell_subtype_percentages[cell_type][cell_subtype])"
+    "        cell_subtype_percentages[cell_type][cell_subtype] = cell_subtype_num_cells[cell_type][cell_subtype]/sum(cell_type_num_cells.values())"
    ]
   },
   {
@@ -163,7 +165,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.6.12"
   }
  },
  "nbformat": 4,

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='capblood-seq-viz',
-    version='1.0.1',
+    version='1.0.2',
     description='Interactive visualization web app for capillary blood data',
     url='https://github.com/ThomsonLab/capblood-seq-viz',
     author='David Brown',