Add nonpharyngeal neuron view; ensure correct ordering of male neuron…

…s in matrix
openworm · Dec 16, 2024 · 0647fa7 · 0647fa7
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diff --git a/.gitignore b/.gitignore
@@ -685,3 +685,21 @@ __pycache__
 /docs/assets/Brittin2021*
 /docs/*_Brittin2021_data*.md
 /clean.sh
+/docs/assets/Test_Nonpharyngeal_Chemical_Exc.json
+/docs/assets/Test_Nonpharyngeal_Chemical_Exc.png
+/docs/assets/Test_Nonpharyngeal_Chemical_Exc_graph.json
+/docs/assets/Test_Nonpharyngeal_Chemical_Exc_graph.png
+/docs/assets/Test_Nonpharyngeal_Chemical_Exc_hiveplot.json
+/docs/assets/Test_Nonpharyngeal_Chemical_Exc_hiveplot.png
+/docs/assets/Test_Nonpharyngeal_Chemical_Inh.json
+/docs/assets/Test_Nonpharyngeal_Chemical_Inh.png
+/docs/assets/Test_Nonpharyngeal_Chemical_Inh_graph.json
+/docs/assets/Test_Nonpharyngeal_Chemical_Inh_graph.png
+/docs/assets/Test_Nonpharyngeal_Chemical_Inh_hiveplot.json
+/docs/assets/Test_Nonpharyngeal_Chemical_Inh_hiveplot.png
+/docs/assets/Test_Nonpharyngeal_Electrical.json
+/docs/assets/Test_Nonpharyngeal_Electrical.png
+/docs/assets/Test_Nonpharyngeal_Electrical_graph.json
+/docs/assets/Test_Nonpharyngeal_Electrical_graph.png
+/docs/assets/Test_Nonpharyngeal_Electrical_hiveplot.json
+/docs/assets/Test_Nonpharyngeal_Electrical_hiveplot.png
diff --git a/cect/Analysis.py b/cect/Analysis.py
@@ -5,22 +5,25 @@
 
 
 def test_bilaterals():
-    from cect.BrittinDataReader import get_instance
+    from cect.White_whole import get_instance
 
     """
-    from cect.White_whole import get_instance
-    from cect.WormNeuroAtlasMAReader import get_instance
-    from cect.WormNeuroAtlasFuncReader import get_instance
-    from cect.Cook2019HermReader import get_instance
     from cect.Cook2019MaleReader import get_instance
+    from cect.Cook2019HermReader import get_instance
     from cect.WitvlietDataReader1 import get_instance
     from cect.WitvlietDataReader8 import get_instance
-    from cect.RipollSanchezDataReader import get_instance
     from cect.TestDataReader import get_instance
+    from cect.SpreadsheetDataReader import get_instance
     from cect.Cook2020DataReader import get_instance
+    from cect.BrittinDataReader import get_instance
+    from cect.WormNeuroAtlasMAReader import get_instance
+    from cect.WormNeuroAtlasFuncReader import get_instance
+    from cect.RipollSanchezDataReader import get_instance
     from cect.ConnectomeView import PHARYNX_VIEW as view
-    from cect.ConnectomeView import NONPHARYNGEAL_NEURONS_VIEW as view"""
+    from cect.ConnectomeView import SOCIAL_VIEW as view
     from cect.ConnectomeView import NEURONS_VIEW as view
+    from cect.ConnectomeView import RAW_VIEW as view"""
+    from cect.ConnectomeView import NONPHARYNGEAL_NEURONS_VIEW as view
 
     print(
         "NOTE: For the sake of this paper, we excluded the pharyngeal neurons from the connectome data for both genders due to their distinction from the somatic nervous system."
@@ -31,7 +34,7 @@ def test_bilaterals():
     cds2 = cds.get_connectome_view(view)
 
     synclass = "Chemical Inh"
-    synclass = "Chemical Exc"
+    synclass = "Chemical Exc" if "Raw" not in view.name else "Chemical"
 
     # synclass = "Acetylcholine"
     # synclass = "Chemical"
@@ -59,22 +62,27 @@ def array_info(conn_array):
     array_info(new_conn_array)
 
     for synclass in [
+        "Chemical",
         "Chemical Exc",
+        "Chemical Inh",
         "Electrical",
         "Contact",
         "Functional",
         "Extrasynaptic",
     ]:
         print("   Adding conns of type: %s" % synclass)
-        conns_cs = cds2.connections[synclass]
-
-        array_info(conns_cs)
-        for i in range(len(conns_cs)):
-            for j in range(len(conns_cs[i])):
-                if (
-                    i != j
-                ):  #  Kim et al 2024: Self-connections are treated as nonexistent (∀𝐴𝑖𝑖 = 0).
-                    new_conn_array[i, j] = new_conn_array[i, j] or conns_cs[i, j] > 0
+        if synclass in cds2.connections:
+            conns_cs = cds2.connections[synclass]
+
+            array_info(conns_cs)
+            for i in range(len(conns_cs)):
+                for j in range(len(conns_cs[i])):
+                    if (
+                        i != j
+                    ):  #  Kim et al 2024: Self-connections are treated as nonexistent (∀𝐴𝑖𝑖 = 0).
+                        new_conn_array[i, j] = (
+                            new_conn_array[i, j] or conns_cs[i, j] > 0
+                        )
 
     amal = "CS+GJ"
     print("Amalgamated array:")

diff --git a/cect/Cells.py b/cect/Cells.py
@@ -501,7 +501,7 @@ def get_cell_notes(cell: str):
 for cell in MALE_HEAD_SENSORY_NEURONS:
     cell_notes[cell] = "male head sensory neuron"
 
-MALE_SENSORY_NEURONS = [
+MALE_NON_HEAD_SENSORY_NEURONS = [
     "R1AL",
     "R1AR",
     "R1BL",
@@ -556,10 +556,10 @@ def get_cell_notes(cell: str):
     "SPVR",
 ]
 
-for cell in MALE_SENSORY_NEURONS:
+for cell in MALE_NON_HEAD_SENSORY_NEURONS:
     cell_notes[cell] = "male sensory neuron"
 
-MALE_INTERNEURONS = [
+MALE_NON_HEAD_INTERNEURONS = [
     "PVV",
     "PVX",
     "PVY",
@@ -595,15 +595,15 @@ def get_cell_notes(cell: str):
 ]
 
 
-for cell in MALE_INTERNEURONS:
+for cell in MALE_NON_HEAD_INTERNEURONS:
     cell_notes[cell] = "male interneuron"
 
 
 MALE_SPECIFIC_NEURONS = (
     MALE_HEAD_INTERNEURONS
+    + MALE_NON_HEAD_INTERNEURONS
     + MALE_HEAD_SENSORY_NEURONS
-    + MALE_INTERNEURONS
-    + MALE_SENSORY_NEURONS
+    + MALE_NON_HEAD_SENSORY_NEURONS
 )
 
 UNKNOWN_FUNCTION_NEURONS = ["CANL", "CANR"]
@@ -1524,7 +1524,9 @@ def get_primary_classification():
                         classification[cell] = cell_type
                 elif cell_type == "interneuron":
                     for cell in (
-                        INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS + MALE_INTERNEURONS
+                        INTERNEURONS_COOK
+                        + MALE_HEAD_INTERNEURONS
+                        + MALE_NON_HEAD_INTERNEURONS
                     ):
                         classification[cell] = cell_type
                 elif cell_type == "motor neuron":
@@ -1534,7 +1536,7 @@ def get_primary_classification():
                     for cell in (
                         SENSORY_NEURONS_COOK
                         + MALE_HEAD_SENSORY_NEURONS
-                        + MALE_SENSORY_NEURONS
+                        + MALE_NON_HEAD_SENSORY_NEURONS
                     ):
                         classification[cell] = cell_type
                 elif cell_type == "odd numbered pharyngeal muscle":
@@ -1955,10 +1957,15 @@ def get_standard_color(cell: str):
         return WA_COLORS["Hermaphrodite"]["Muscle"]["odd numbered pharyngeal muscle"]
     elif cell in EVEN_PHARYNGEAL_MUSCLE_NAMES:
         return WA_COLORS["Hermaphrodite"]["Muscle"]["even numbered pharyngeal muscle"]
-    elif cell in INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS + MALE_INTERNEURONS:
+    elif (
+        cell in INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS + MALE_NON_HEAD_INTERNEURONS
+    ):
         return WA_COLORS["Hermaphrodite"]["Nervous Tissue"]["interneuron"]
     elif (
-        cell in SENSORY_NEURONS_COOK + MALE_HEAD_SENSORY_NEURONS + MALE_SENSORY_NEURONS
+        cell
+        in SENSORY_NEURONS_COOK
+        + MALE_HEAD_SENSORY_NEURONS
+        + MALE_NON_HEAD_SENSORY_NEURONS
     ):
         return WA_COLORS["Hermaphrodite"]["Nervous Tissue"]["sensory neuron"]
     elif cell in MOTORNEURONS_COOK:
@@ -2430,7 +2437,7 @@ def _generate_cell_table(cell_type: str, cells: List[str]):
                                     cell_type,
                                     INTERNEURONS_COOK
                                     + MALE_HEAD_INTERNEURONS
-                                    + MALE_INTERNEURONS,
+                                    + MALE_NON_HEAD_INTERNEURONS,
                                 )
                             )
                         elif cell_type == "motor neuron":
@@ -2441,7 +2448,7 @@ def _generate_cell_table(cell_type: str, cells: List[str]):
                                     cell_type,
                                     SENSORY_NEURONS_COOK
                                     + MALE_HEAD_SENSORY_NEURONS
-                                    + MALE_SENSORY_NEURONS,
+                                    + MALE_NON_HEAD_SENSORY_NEURONS,
                                 )
                             )
                         elif cell_type == "odd numbered pharyngeal muscle":

diff --git a/cect/Comparison.py b/cect/Comparison.py
@@ -179,8 +179,7 @@ def generate_comparison_page(quick: bool, color_table=True, dataset_pages=True):
         readers["Witvliet4"] = ["cect.WitvlietDataReader4", "Witvliet_2021"]
         readers["Witvliet5"] = ["cect.WitvlietDataReader5", "Witvliet_2021"]
         readers["Witvliet6"] = ["cect.WitvlietDataReader6", "Witvliet_2021"]
-
-    readers["Witvliet7"] = ["cect.WitvlietDataReader7", "Witvliet_2021"]
+        readers["Witvliet7"] = ["cect.WitvlietDataReader7", "Witvliet_2021"]
 
     readers["Witvliet8"] = ["cect.WitvlietDataReader8", "Witvliet_2021"]
 

diff --git a/cect/ConnectomeView.py b/cect/ConnectomeView.py
@@ -7,6 +7,10 @@
 from cect.Cells import INTERNEURONS_NONPHARYNGEAL_COOK
 from cect.Cells import UNKNOWN_FUNCTION_NEURONS
 from cect.Cells import MALE_SPECIFIC_NEURONS
+from cect.Cells import MALE_HEAD_INTERNEURONS
+from cect.Cells import MALE_NON_HEAD_INTERNEURONS
+from cect.Cells import MALE_HEAD_SENSORY_NEURONS
+from cect.Cells import MALE_NON_HEAD_SENSORY_NEURONS
 from cect.Cells import PREFERRED_MUSCLE_NAMES
 from cect.Cells import ALL_NON_NEURON_MUSCLE_CELLS
 
@@ -156,24 +160,41 @@ def get_index_of_cell(self, cell):
 NEURONS_VIEW = View(
     "Neurons",
     "Neurons",
-    "All 302 hermaphrodite neurons (whether present or not in the connectome dataset)",
+    "All 302 **hermaphrodite** neurons (whether present or not in the connectome dataset)",
     [],
     EXC_INH_GJ_FUNC_CONT_SYN_CLASSES,
 )
 
-NONPHARYNGEAL_NEURONS_VIEW = View(
+NONPHARYNGEAL_NEURONS_HERM_VIEW = View(
     "Nonpharyngeal",
     "Nonpharyngeal Neurons",
-    "All neurons except those in the pharynx",
+    "All **hermaphrodite** neurons except those in the pharynx",
+    [],
+    EXC_INH_GJ_FUNC_CONT_SYN_CLASSES,
+    only_show_existing_nodes=False,
+)
+
+NONPHARYNGEAL_NEURONS_HM_VIEW = View(
+    "Nonpharyngeal",
+    "Nonpharyngeal Neurons",
+    "All neurons (herm. & male) except those in the pharynx",
     [],
     EXC_INH_GJ_FUNC_CONT_SYN_CLASSES,
     only_show_existing_nodes=False,
 )
 
 for cell in (
     sorted(PHARYNGEAL_NEURONS)
-    + sorted(SENSORY_NEURONS_NONPHARYNGEAL_COOK)
-    + sorted(INTERNEURONS_NONPHARYNGEAL_COOK)
+    + sorted(
+        SENSORY_NEURONS_NONPHARYNGEAL_COOK
+        + MALE_HEAD_SENSORY_NEURONS
+        + MALE_NON_HEAD_SENSORY_NEURONS
+    )
+    + sorted(
+        INTERNEURONS_NONPHARYNGEAL_COOK
+        + MALE_HEAD_INTERNEURONS
+        + MALE_NON_HEAD_INTERNEURONS
+    )
     + sorted(
         HEAD_MOTORNEURONS_COOK
         + VENTRAL_CORD_MOTORNEURONS
@@ -183,23 +204,21 @@ def get_index_of_cell(self, cell):
     )
     + sorted(UNKNOWN_FUNCTION_NEURONS)
 ):
-    NEURONS_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell)))
     RAW_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell)))
+
+    if cell not in MALE_SPECIFIC_NEURONS:
+        NEURONS_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell)))
+
     if cell not in PHARYNGEAL_NEURONS:
-        NONPHARYNGEAL_NEURONS_VIEW.node_sets.append(
+        if cell not in MALE_SPECIFIC_NEURONS:
+            NONPHARYNGEAL_NEURONS_HERM_VIEW.node_sets.append(
+                NodeSet(cell, [cell], get_standard_color(cell))
+            )
+        NONPHARYNGEAL_NEURONS_HM_VIEW.node_sets.append(
             NodeSet(cell, [cell], get_standard_color(cell))
         )
 
-for cell in sorted(MALE_SPECIFIC_NEURONS):
-    NONPHARYNGEAL_NEURONS_VIEW.node_sets.append(
-        NodeSet(cell, [cell], get_standard_color(cell))
-    )
-
-for cell in (
-    sorted(MALE_SPECIFIC_NEURONS)
-    + sorted(PREFERRED_MUSCLE_NAMES)
-    + sorted(ALL_NON_NEURON_MUSCLE_CELLS)
-):
+for cell in sorted(PREFERRED_MUSCLE_NAMES) + sorted(ALL_NON_NEURON_MUSCLE_CELLS):
     RAW_VIEW.node_sets.append(NodeSet(cell, [cell], get_standard_color(cell)))
 
 assert len(NEURONS_VIEW.node_sets) == 302
@@ -491,6 +510,7 @@ def get_index_of_cell(self, cell):
     RAW_VIEW,
     NEURONS_VIEW,
     PHARYNX_VIEW,
+    NONPHARYNGEAL_NEURONS_HERM_VIEW,
     SOCIAL_VIEW,
     ESCAPE_VIEW,
     COOK_FIG3_VIEW,
@@ -547,7 +567,7 @@ def get_index_of_cell(self, cell):
     print(tdr_instance.get_connectome_view(ESCAPE_VIEW).summary())
 
     print("------- Nonpharyngeal ---------")
-    print(tdr_instance.get_connectome_view(NONPHARYNGEAL_NEURONS_VIEW).summary())
+    print(tdr_instance.get_connectome_view(NONPHARYNGEAL_NEURONS_HM_VIEW).summary())
 
     """
     from cect.Cells import ALL_PREFERRED_CELL_NAMES

diff --git a/cect/data/all_cell_info.csv b/cect/data/all_cell_info.csv
@@ -303,10 +303,6 @@ VD8,Ventral cord motor neuron,Ventral D-type Motor Neuron 8,P7.app,"Ventralcord
 VD9,Ventral cord motor neuron,Ventral D-type Motor Neuron 9,P8.app,"Ventral cord motor neuron, innervates vent body muscles, reciprocal inhibitor"
 MCML,Male head interneuron,Mystery Cell of the Male Left,AmsoL,Male specific interneuron
 MCMR,Male head interneuron,Mystery Cell of the Male Right,AmsoR,Male specific interneuron
-CEMDL,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Left,AB plaaaaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
-CEMDR,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Right,AB arpapaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
-CEMVL,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Left,AB plpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
-CEMVR,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Right,AB prpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
 PVV,Male interneuron,Posterior Ventral Process V,P11.paaa,"Male specific motor neuron, pre-anal ganglion"
 PVX,Male interneuron,Posterior Ventral Process X,P12.aap,"Male specific interneuron, cell body in pre-anal ganglion, postsynaptic in ring and ventral cord"
 PVY,Male interneuron,Posterior Ventral Process Y,P11.paap,"Male specific interneuron, cell body in pre-anal ganglion"
@@ -339,6 +335,10 @@ CP06,Male interneuron,"C-type Neuron, Posterior Daughter after Division 6",P8.aa
 CP07,Male interneuron,"C-type Neuron, Posterior Daughter after Division 7",P9.aapp,Male specific motor neuron in ventral cord
 CP08,Male interneuron,"C-type Neuron, Posterior Daughter after Division 8",P10.aapp,"Male specific interneuron, projects into preanal ganglion"
 CP09,Male interneuron,"C-type Neuron, Posterior Daughter after Division 9",P11.aapp,"Male specific interneuron, projects into preanal ganglion"
+CEMDL,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Left,AB plaaaaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
+CEMDR,Male head sensory neuron,CEphalic Male Sensory Neuron Dorsal Right,AB arpapaaap,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
+CEMVL,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Left,AB plpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
+CEMVR,Male head sensory neuron,CEphalic Male Sensory Neuron Ventral Right,AB prpaapapp,"Male specific cephalic neurons (programmed cell death in hermaphrodite embryo) open to outside, possible function in male chemotaxis toward hermaphrodite"
 R1AL,Male sensory neuron,Ray 1 Neuron A Left,"V5L.pppppaaa, (R1.aaaL)","Male sensory rays, neuron, striated rootlet, cell body in left lumbar ganglion"
 R1AR,Male sensory neuron,Ray 1 Neuron A Right,"V5R.pppppaaa, (R1.aaaR)","Male sensory rays, neuron, striated rootlet, cell body in right lumbar ganglion"
 R1BL,Male sensory neuron,Ray 1 Neuron B Left,"V5L.pppppapa, (R1.apaL)","Male sensory rays, neuron, darkly staining tip, open to outside, cell body in left lumbar ganglion"