Improved Randi 2023 colours

openworm · Sep 3, 2024 · cd24c36 · cd24c36
1 parent 15ecba1
commit cd24c36
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Showing 189 changed files with 122,210 additions and 315 deletions.
diff --git a/cect/Cells.py b/cect/Cells.py
@@ -1702,6 +1702,8 @@ def _generate_cell_table(cell_type, cells):
 
     fig_md = ""
 
+    verbose = False
+
     for syn_summary in syn_summaries:
         fig = go.Figure()
         fig.layout.showlegend = True
@@ -1723,10 +1725,11 @@ def _generate_cell_table(cell_type, cells):
                         conns_here = connectome.get_connections_from(cell, syn_type)
                     else:
                         conns_here = connectome.get_connections_to(cell, syn_type)
-                    print_(
-                        "Conns: %i for %s of type %s (%s)"
-                        % (len(conns_here), cell, syn_type, syn_summary)
-                    )
+                    if verbose:
+                        print_(
+                            "Conns: %i for %s of type %s (%s)"
+                            % (len(conns_here), cell, syn_type, syn_summary)
+                        )
                     total_y += len(conns_here)
 
                 y.append(total_y)

diff --git a/cect/ConnectomeDataset.py b/cect/ConnectomeDataset.py
@@ -253,9 +253,15 @@ def to_plotly_matrix_fig(self, synclass, view, color_continuous_scale=None):
 
         conn_array = self.connections[synclass]
 
-        color_continuous_scale = (
-            POS_NEG_COLORMAP if synclass == "Functional" else DEFAULT_COLORMAP
-        )
+        zmin = np.min(conn_array)
+        zmax = np.max(conn_array)
+        color_continuous_scale = DEFAULT_COLORMAP
+
+        if synclass == "Functional":
+            color_continuous_scale = POS_NEG_COLORMAP
+            largest = max(abs(zmin), abs(zmax))
+            zmin = -1 * largest
+            zmax = largest
 
         def get_color_html(color, node):
             return f'<span style="color:{color};">{node}</span>'
@@ -278,11 +284,14 @@ def get_color_html(color, node):
 
         fig = px.imshow(
             conn_array,
-            labels=dict(x="Postsynaptic", y="Presynaptic", color="Synapses"),
+            labels=dict(x="Postsynaptic", y="Presynaptic", color="Weight"),
             x=x_ticktext,
             y=y_ticktext,
             color_continuous_scale=color_continuous_scale,
+            zmin=zmin,
+            zmax=zmax,
         )
+
         fig.update(
             data=[
                 {

diff --git a/cect/ConnectomeReader.py b/cect/ConnectomeReader.py
@@ -12,7 +12,7 @@
 from cect.Cells import PREFERRED_MUSCLE_NAMES
 
 DEFAULT_COLORMAP = ["white", "green", "black"]
-POS_NEG_COLORMAP = "Spectral_r"
+POS_NEG_COLORMAP = ["darkblue", "blue", "white", "red", "darkred"]
 
 
 def convert_to_preferred_muscle_name(muscle):

diff --git a/cect/ConnectomeView.py b/cect/ConnectomeView.py
@@ -118,7 +118,8 @@ def get_index_of_cell(self, cell):
     RAW_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell)))
 
 
-FULL_VIEW = View("Full View", [], EXC_INH_GJ_SYN_CLASSES)
+FULL_VIEW = View("Full View", [], EXC_INH_GJ_FUNC_SYN_CLASSES)
+
 for cell in (
     sorted(SENSORY_NEURONS_COOK)
     + sorted(INTERNEURONS_NONPHARYNGEAL_COOK)

diff --git a/docs/Randi2023_data.md b/docs/Randi2023_data.md
@@ -13,6 +13,12 @@ Data extracted from the **WormNeuroAtlas package** for functional connectivity
         ```
 
 === "Full View"
+    === "Functional"
+
+        ```plotly
+        ---8<-- "./assets/Randi2023_Full View_Functional.json"
+        ```
+
 === "Pharynx View"
     === "Functional"
 

diff --git a/docs/Randi2023_data_graph.md b/docs/Randi2023_data_graph.md
@@ -13,6 +13,12 @@ Data extracted from the **WormNeuroAtlas package** for functional connectivity
         ```
 
 === "Full View"
+    === "Functional"
+
+        ```plotly
+        ---8<-- "./assets/Randi2023_Full View_Functional_graph.json"
+        ```
+
 === "Pharynx View"
     === "Functional"
 

diff --git a/docs/assets/Cook2019Herm_Full View_Chemical_Exc.json b/docs/assets/Cook2019Herm_Full View_Chemical_Exc.json
@@ -96734,9 +96734,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 75.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Full View_Chemical_Inh.json b/docs/assets/Cook2019Herm_Full View_Chemical_Inh.json
@@ -96734,9 +96734,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 13.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Full View_Electrical.json b/docs/assets/Cook2019Herm_Full View_Electrical.json
@@ -96734,9 +96734,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 250.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Pharynx View_Chemical_Exc.json b/docs/assets/Cook2019Herm_Pharynx View_Chemical_Exc.json
@@ -497,9 +497,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 34.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Pharynx View_Electrical.json b/docs/assets/Cook2019Herm_Pharynx View_Electrical.json
@@ -497,9 +497,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 11.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Raw Data_Chemical.json b/docs/assets/Cook2019Herm_Raw Data_Chemical.json
@@ -225638,9 +225638,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 142.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Raw Data_Electrical.json b/docs/assets/Cook2019Herm_Raw Data_Electrical.json
@@ -225638,9 +225638,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 401.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Small View_Chemical.json b/docs/assets/Cook2019Herm_Small View_Chemical.json
@@ -374,9 +374,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 2341.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Small View_Electrical.json b/docs/assets/Cook2019Herm_Small View_Electrical.json
@@ -374,9 +374,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 1894.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Social View_Chemical_Exc.json b/docs/assets/Cook2019Herm_Social View_Chemical_Exc.json
@@ -94,9 +94,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 6.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Herm_Social View_Electrical.json b/docs/assets/Cook2019Herm_Social View_Electrical.json
@@ -94,9 +94,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 5.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Full View_Chemical_Exc.json b/docs/assets/Cook2019Male_Full View_Chemical_Exc.json
@@ -96734,9 +96734,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 171.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Full View_Chemical_Inh.json b/docs/assets/Cook2019Male_Full View_Chemical_Inh.json
@@ -96734,9 +96734,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 12.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Full View_Electrical.json b/docs/assets/Cook2019Male_Full View_Electrical.json
@@ -96734,9 +96734,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 250.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Pharynx View_Chemical_Exc.json b/docs/assets/Cook2019Male_Pharynx View_Chemical_Exc.json
@@ -497,9 +497,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 34.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Pharynx View_Electrical.json b/docs/assets/Cook2019Male_Pharynx View_Electrical.json
@@ -497,9 +497,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 11.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Raw Data_Chemical.json b/docs/assets/Cook2019Male_Raw Data_Chemical.json
@@ -342238,9 +342238,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 194.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Raw Data_Electrical.json b/docs/assets/Cook2019Male_Raw Data_Electrical.json
@@ -342238,9 +342238,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 400.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Small View_Chemical.json b/docs/assets/Cook2019Male_Small View_Chemical.json
@@ -374,9 +374,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 2318.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Small View_Electrical.json b/docs/assets/Cook2019Male_Small View_Electrical.json
@@ -374,9 +374,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 2274.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Social View_Chemical_Exc.json b/docs/assets/Cook2019Male_Social View_Chemical_Exc.json
@@ -94,9 +94,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 2.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [

diff --git a/docs/assets/Cook2019Male_Social View_Electrical.json b/docs/assets/Cook2019Male_Social View_Electrical.json
@@ -94,9 +94,11 @@
   ],
   "layout": {
     "coloraxis": {
+      "cmax": 6.0,
+      "cmin": 0.0,
       "colorbar": {
         "title": {
-          "text": "Synapses"
+          "text": "Weight"
         }
       },
       "colorscale": [