Merge pull request #29 from pgleeson/main

Improved cell pages

cect/CellInfo.py

@@ -7,12 +7,15 @@
 from cect.Cells import get_cell_wormatlas_link
 from cect.Cells import get_cell_osbv1_link
 from cect.Cells import are_bilateral_pair
+from cect.Cells import is_any_neuron
+from cect.Cells import get_primary_classification
 
 
 from cect import print_
 # from pprint import pprint
 
 import pandas as pd
+import csv
 
 pd.options.plotting.backend = "plotly"
 
@@ -66,18 +69,77 @@ def get_weight_table_markdown(w):
             marker=dict(size=4), marker_symbol="circle", mode="lines+markers"
         )
         indent = ""
-        fig_md = f"\n{indent}<br/>\n{indent}```plotly\n{indent}{fig.to_json()}\n{indent}```\n"
+        fig_md = f"\n{indent}```plotly\n{indent}{fig.to_json()}\n{indent}```\n"
     else:
         fig_md = ""
 
     return "%s\n\n%s" % (df_all.to_markdown(), fig_md)
 
 
+def load_individual_neuron_info():
+    # From https://wormatlas.org/neurons/Individual%20Neurons/Neuronframeset.html
+    filename = "cect/data/IndividualNeurons.csv"
+    cell_info = {}
+    with open(filename) as csvfile:
+        reader = csv.reader(csvfile, delimiter=";")
+        print(reader)
+
+        for row in reader:
+            print(", ".join(row))
+            if not row[0].startswith("#"):
+                cell_info[row[0]] = (row[1].strip(), row[2].strip(), row[3].strip())
+
+    return cell_info
+
+
 def generate_cell_info_pages(connectomes):
+    cell_data = load_individual_neuron_info()
+    cell_classification = get_primary_classification()
+
     for cell in ALL_PREFERRED_CELL_NAMES:
+        print_("Generating individual cell page for: %s" % cell)
+
         cell_info = '---\ntitle: "Cell: %s"\n---\n\n' % cell
 
-        cell_info += "**%s**\n\n" % (get_cell_notes(cell))
+        # TODO: investigate  DX1, DX2, DX3, EF1, EF2, EF3
+        if is_any_neuron(cell) and "DX" not in cell and "EF" not in cell:
+            cell_ref = (
+                cell
+                if not (
+                    (cell.startswith("CA") or cell.startswith("CP")) and cell[2] == "0"
+                )
+                else "%s%s" % (cell[:2], cell[-1])
+            )  # CA04 -> CA4 etc.
+            ackr = cell_data[cell_ref][0]
+            from_ = 0
+            for c in cell:
+                # print('Replacing %s (from %s) in %s'%(c,from_,ackr))
+                if c in ackr:
+                    ii = ackr.index(c, from_)
+                    ackr = "%s<b>%s</b>%s" % (ackr[:ii], ackr[ii], ackr[ii + 1 :])
+                    from_ = ii + 1
+
+            cell_info += "**%s**\n\n" % (cell_data[cell_ref][2])
+            cell_info += '<p class="subtext">%s&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;' % (
+                ackr
+            )
+            cell_info += "Lineage: <b>%s</b></p>\n\n" % (cell_data[cell_ref][1])
+        else:
+            cell_info += "**%s**\n\n" % (get_cell_notes(cell))
+
+        cell_info += (
+            '<p class="subtext"><a href="../Cook_2019">Cook 2019</a> classification: <b>%s</b>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'
+            % (get_cell_notes(cell))
+        )
+        cc = cell_classification[cell]
+        cell_info += (
+            'All cells of type: <a href="../Cells/#%s"><b>%s</b></a></p>\n\n'
+            % (
+                cc.replace(" ", "-").replace("(", "").replace(")", ""),
+                cc[0].upper() + cc[1:],
+            )
+        )
+
         cell_info += "%s " % (
             get_cell_wormatlas_link(cell, text="Info on WormAtlas", button=True)
         )
@@ -198,4 +260,5 @@ def generate_cell_info_pages(connectomes):
 
     connectomes = {"White_whole": cds_white, "Witvliet8": cds_w8}
 
+    # load_individual_neuron_info()
     generate_cell_info_pages(connectomes)

cect/Cells.py

@@ -1109,14 +1109,6 @@ def get_cell_notes(cell):
 
 VULVAL_MUSCLE_NAMES = [
     "MVULVA",
-    "um2AL",
-    "um2AR",
-    "um1AL",
-    "um1AR",
-    "um1PL",
-    "um1PR",
-    "um2PL",
-    "um2PR",
     "vm1AL",
     "vm1PL",
     "vm1PR",
@@ -1129,6 +1121,19 @@ def get_cell_notes(cell):
 for cell in VULVAL_MUSCLE_NAMES:
     cell_notes[cell] = "vulval muscle"
 
+UTERINE_MUSCLE_NAMES = [
+    "um2AL",
+    "um2AR",
+    "um1AL",
+    "um1AR",
+    "um1PL",
+    "um1PR",
+    "um2PL",
+    "um2PR",
+]
+for cell in UTERINE_MUSCLE_NAMES:
+    cell_notes[cell] = "uterine muscle"
+
 ODD_PHARYNGEAL_MUSCLE_NAMES = [
     "pm1",
     "pm3D",
@@ -1308,6 +1313,7 @@ def get_cell_notes(cell):
     BODY_WALL_MUSCLE_NAMES
     + PHARYNGEAL_MUSCLE_NAMES
     + VULVAL_MUSCLE_NAMES
+    + UTERINE_MUSCLE_NAMES
     + ANAL_SPHINCTER_MUSCLES
     + MALE_SPECIFIC_MUSCLES
     + INTESTINAL_MUSCLES
@@ -1319,6 +1325,7 @@ def get_cell_notes(cell):
 COOK_GROUPING_1["Other muscles"] = (
     PHARYNGEAL_MUSCLE_NAMES
     + VULVAL_MUSCLE_NAMES
+    + UTERINE_MUSCLE_NAMES
     + ANAL_SPHINCTER_MUSCLES
     + UNSPECIFIED_BODY_WALL_MUSCLES
 )
@@ -1343,7 +1350,7 @@ def get_cell_notes(cell):
 ]
 
 for cell in CEPSH_CELLS:
-    cell_notes[cell] = "glial"
+    cell_notes[cell] = "sheath cell other than amphid sheath and phasmid"
 
 GLIAL_CELLS = GLR_CELLS + CEPSH_CELLS
 
@@ -1464,6 +1471,172 @@ def get_cell_notes(cell):
 )
 
 
+def get_primary_classification():
+    classification = {}
+
+    for sex in WA_COLORS:
+        for cell_class in WA_COLORS[sex]:
+            for cell_type in WA_COLORS[sex][cell_class]:
+                print_(" - %s/%s/%s" % (sex, cell_class, cell_type))
+
+                if cell_type == "body wall muscle":
+                    for cell in BODY_WALL_MUSCLE_NAMES + UNSPECIFIED_BODY_WALL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "vulval muscle":
+                    for cell in VULVAL_MUSCLE_NAMES:
+                        classification[cell] = cell_type
+                elif cell_type == "uterine muscle":
+                    for cell in UTERINE_MUSCLE_NAMES:
+                        classification[cell] = cell_type
+                elif cell_type == "interneuron":
+                    for cell in (
+                        INTERNEURONS_COOK + MALE_HEAD_INTERNEURONS + MALE_INTERNEURONS
+                    ):
+                        classification[cell] = cell_type
+                elif cell_type == "motor neuron":
+                    for cell in MOTORNEURONS_COOK:
+                        classification[cell] = cell_type
+                elif cell_type == "sensory neuron":
+                    for cell in (
+                        SENSORY_NEURONS_COOK
+                        + MALE_HEAD_SENSORY_NEURONS
+                        + MALE_SENSORY_NEURONS
+                    ):
+                        classification[cell] = cell_type
+                elif cell_type == "odd numbered pharyngeal muscle":
+                    for cell in ODD_PHARYNGEAL_MUSCLE_NAMES:
+                        classification[cell] = cell_type
+                elif cell_type == "even numbered pharyngeal muscle":
+                    for cell in EVEN_PHARYNGEAL_MUSCLE_NAMES:
+                        classification[cell] = cell_type
+                elif cell_type == "polymodal neuron":
+                    for cell in PHARYNGEAL_POLYMODAL_NEURONS:
+                        classification[cell] = cell_type
+                elif cell_type == "marginal cells (mc) of the pharynx":
+                    for cell in PHARYNGEAL_MARGINAL_CELLS:
+                        classification[cell] = cell_type
+                elif cell_type == "pharyngeal epithelium":
+                    for cell in PHARYNGEAL_EPITHELIUM + PHARYNGEAL_GLIAL_CELL:
+                        classification[cell] = cell_type  # TODO: check!
+                elif cell_type == "basement membrane":
+                    for cell in PHARYNGEAL_BASEMENT_MEMBRANE:
+                        classification[cell] = cell_type  # TODO: check!
+                elif cell_type == "neuron with unknown function":
+                    for cell in UNKNOWN_FUNCTION_NEURONS:
+                        classification[cell] = cell_type
+                elif cell_type == "sheath cell other than amphid sheath and phasmid":
+                    for cell in CEPSH_CELLS:
+                        classification[cell] = cell_type
+                elif cell_type == "excretory cell":
+                    for cell in EXCRETORY_CELL:
+                        classification[cell] = cell_type
+                elif cell_type == "sphincter and anal depressor muscle":
+                    for cell in ANAL_SPHINCTER_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "gland cell":
+                    for cell in EXCRETORY_GLAND:
+                        classification[cell] = cell_type
+                elif cell_type == "head mesodermal cell":
+                    for cell in HEAD_MESODERMAL_CELL:
+                        classification[cell] = cell_type
+                elif cell_type == "hypodermis":
+                    for cell in HYPODERMIS:
+                        classification[cell] = cell_type
+                elif cell_type == "intestinal cells":
+                    for cell in INTESTINE:
+                        classification[cell] = cell_type
+                elif cell_type == "intestinal muscle":
+                    for cell in INTESTINAL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "GLR cell":
+                    for cell in GLR_CELLS:
+                        classification[cell] = cell_type
+                elif cell_type == "diagonal muscles":
+                    for cell in MALE_DIAGONAL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "posterior outer longitudinal muscles":
+                    for cell in MALE_POSTERIOR_OUTER_LONGITUDINAL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "anterior inner longitudinal muscles":
+                    for cell in MALE_ANTERIOR_INNER_LONGITUDINAL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "posterior inner longitudinal muscles":
+                    for cell in MALE_POSTERIOR_INNER_LONGITUDINAL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "caudal inner longitudinal muscles":
+                    for cell in MALE_CAUDAL_LONGITUDINAL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "spicule retractor muscles":
+                    for cell in (
+                        MALE_VENTRAL_SPICULE_RETRACTOR + MALE_DORSAL_SPICULE_RETRACTOR
+                    ):
+                        classification[cell] = cell_type
+                elif cell_type == "spicule protractor muscles":
+                    for cell in (
+                        MALE_VENTRAL_SPICULE_PROTRACTOR + MALE_DORSAL_SPICULE_PROTRACTOR
+                    ):
+                        classification[cell] = cell_type
+                elif cell_type == "gubernacular retractor muscles":
+                    for cell in MALE_GUBERNACULAR_RETRACTOR_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "gubernacular erector muscles":
+                    for cell in MALE_GUBERNACULAR_ERECTOR_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "anterior oblique muscles":
+                    for cell in MALE_ANTERIOR_OBLIQUE_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "posterior oblique muscles":
+                    for cell in MALE_POSTERIOR_OBLIQUE_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "vas deferens":
+                    for cell in GONAD_CELL:
+                        classification[cell] = cell_type
+                elif cell_type == "proctodeum":
+                    for cell in PROCTODEUM_CELL:
+                        classification[cell] = cell_type
+                elif cell_type == "diagonal muscles":
+                    for cell in MALE_DIAGONAL_MUSCLES:
+                        classification[cell] = cell_type
+                elif cell_type == "ray structural cell":
+                    for cell in MALE_RAY_STRUCTURAL_CELLS:
+                        classification[cell] = cell_type
+                elif cell_type in [
+                    "General code for neuronal tissue if subtype is unspecified",
+                    "vulval epithelium",
+                    "germline",
+                    "DTC and somatic gonad",
+                    "embryo",
+                    "uterus",
+                    "spermatheca",
+                    "spermatheca-uterine valve",
+                    "excretory pore cell",
+                    "duct cell",
+                    "excretory duct",
+                    "seam cell",
+                    "socket cell, XXX cells",
+                    "amphid sheath and phasmid sheath",
+                    "pharyngeal-intestinal valve, intestinal rectal valve",
+                    "arcade cell",
+                    "rectal epithelium (U, F, K, K', Y, B)",
+                    "rectal gland, pharyngeal glands",
+                    "pseudocoelomic space",
+                    "coeloemocyte",
+                    "anterior outer longitudinal muscles",
+                    "seminal vesicle",
+                    "sheath cell (spicules, hook or post-cloacal sensilla)",
+                    "socket cell (spicules, hook or post-cloacal sensilla)",
+                ]:
+                    print_(
+                        "No synaptic connnections to cells of type %s..?" % cell_type
+                    )
+                else:
+                    raise Exception("Cell type %s not handled" % cell_type)
+    for cell in ALL_PREFERRED_CELL_NAMES:
+        assert cell in classification
+
+    return classification
+
+
 def is_known_cell(cell):
     return cell in ALL_PREFERRED_CELL_NAMES
 
@@ -1705,6 +1878,8 @@ def get_standard_color(cell):
         return WA_COLORS["Hermaphrodite"]["Muscle"]["body wall muscle"]
     elif cell in VULVAL_MUSCLE_NAMES:
         return WA_COLORS["Hermaphrodite"]["Muscle"]["vulval muscle"]
+    elif cell in UTERINE_MUSCLE_NAMES:
+        return WA_COLORS["Hermaphrodite"]["Muscle"]["uterine muscle"]
     elif cell in ODD_PHARYNGEAL_MUSCLE_NAMES:
         return WA_COLORS["Hermaphrodite"]["Muscle"]["odd numbered pharyngeal muscle"]
     elif cell in EVEN_PHARYNGEAL_MUSCLE_NAMES:
@@ -1906,6 +2081,9 @@ def get_cell_wormatlas_link(cell_name, html=False, text=None, button=False):
     elif cell_name in VULVAL_MUSCLE_NAMES:
         url = "https://www.wormatlas.org/hermaphrodite/egglaying%20apparatus/Eggframeset.html"
 
+    elif cell_name in UTERINE_MUSCLE_NAMES:
+        url = "https://www.wormatlas.org/hermaphrodite/egglaying%20apparatus/jump.html?newLink=mainframe.htm&newAnchor=Theuterus2"
+
     elif cell_name in ANAL_SPHINCTER_MUSCLES:
         url = "https://www.wormatlas.org/hermaphrodite/excretory/Excframeset.html"
 
@@ -2165,6 +2343,10 @@ def _generate_cell_table(cell_type, cells):
                             f.write(
                                 _generate_cell_table(cell_type, VULVAL_MUSCLE_NAMES)
                             )
+                        elif cell_type == "uterine muscle":
+                            f.write(
+                                _generate_cell_table(cell_type, UTERINE_MUSCLE_NAMES)
+                            )
                         elif cell_type == "interneuron":
                             f.write(
                                 _generate_cell_table(
@@ -2338,3 +2520,34 @@ def _generate_cell_table(cell_type, cells):
                                     cell_type, MALE_RAY_STRUCTURAL_CELLS
                                 )
                             )
+                        elif cell_type in [
+                            "vulval epithelium",
+                            "germline",
+                            "DTC and somatic gonad",
+                            "embryo",
+                            "uterus",
+                            "spermatheca",
+                            "spermatheca-uterine valve",
+                            "excretory pore cell",
+                            "duct cell",
+                            "excretory duct",
+                            "seam cell",
+                            "socket cell, XXX cells",
+                            "amphid sheath and phasmid sheath",
+                            "pharyngeal-intestinal valve, intestinal rectal valve",
+                            "arcade cell",
+                            "rectal epithelium (U, F, K, K', Y, B)",
+                            "rectal gland, pharyngeal glands",
+                            "pseudocoelomic space",
+                            "coeloemocyte",
+                            "anterior outer longitudinal muscles",
+                            "seminal vesicle",
+                            "sheath cell (spicules, hook or post-cloacal sensilla)",
+                            "socket cell (spicules, hook or post-cloacal sensilla)",
+                        ]:
+                            print_(
+                                "No synaptic connnections to cells of type %s..?"
+                                % cell_type
+                            )
+                        else:
+                            raise Exception("Cell type %s not handled" % cell_type)