Merge pull request #12 from josenimo/main

v1.0 plotting, slider, and gates table

gates.csv

@@ -0,0 +1,121 @@
+sample_id,marker_id,gate_value
+68,Rabbit IgG,3478.531304347826
+68,Goat IgG,0.0
+68,Mouse IgG,0.0
+68,CD73,0.0
+68,CD107B,0.0
+68,MART1,0.0
+68,KI67,0.0
+68,pan-CK,0.0
+68,CD45,0.0
+68,ECAD,0.0
+68,aSMA,0.0
+68,CD56,0.0
+68,CD13,0.0
+68,CD63,0.0
+68,CD32,0.0
+68,CDKN1A,0.0
+68,CCNA2,0.0
+68,CDKN1C,0.0
+68,PCNA_1,0.0
+68,pAUR,0.0
+68,CDKN1B_1,0.0
+68,CCND1,0.0
+68,cPARP,0.0
+68,CDKN1B_2,0.0
+68,pCREB,0.0
+68,CCNB1,0.0
+68,CCNE,0.0
+68,PCNA_2,3487.7142857142853
+68,CDK2,0.0
+68,CDKN2A,0.0
+1,Rabbit IgG,0.0
+1,Goat IgG,0.0
+1,Mouse IgG,0.0
+1,CD73,0.0
+1,CD107B,0.0
+1,MART1,0.0
+1,KI67,0.0
+1,pan-CK,0.0
+1,CD45,0.0
+1,ECAD,0.0
+1,aSMA,0.0
+1,CD56,0.0
+1,CD13,0.0
+1,CD63,0.0
+1,CD32,0.0
+1,CDKN1A,0.0
+1,CCNA2,0.0
+1,CDKN1C,0.0
+1,PCNA_1,0.0
+1,pAUR,0.0
+1,CDKN1B_1,0.0
+1,CCND1,0.0
+1,cPARP,0.0
+1,CDKN1B_2,0.0
+1,pCREB,0.0
+1,CCNB1,0.0
+1,CCNE,0.0
+1,PCNA_2,0.0
+1,CDK2,0.0
+1,CDKN2A,0.0
+18,Rabbit IgG,2666.8921052631576
+18,Goat IgG,0.0
+18,Mouse IgG,0.0
+18,CD73,0.0
+18,CD107B,0.0
+18,MART1,0.0
+18,KI67,0.0
+18,pan-CK,0.0
+18,CD45,0.0
+18,ECAD,0.0
+18,aSMA,0.0
+18,CD56,0.0
+18,CD13,578.2247191011238
+18,CD63,0.0
+18,CD32,0.0
+18,CDKN1A,0.0
+18,CCNA2,0.0
+18,CDKN1C,0.0
+18,PCNA_1,0.0
+18,pAUR,0.0
+18,CDKN1B_1,0.0
+18,CCND1,0.0
+18,cPARP,0.0
+18,CDKN1B_2,0.0
+18,pCREB,0.0
+18,CCNB1,0.0
+18,CCNE,0.0
+18,PCNA_2,0.0
+18,CDK2,0.0
+18,CDKN2A,0.0
+15,Rabbit IgG,0.0
+15,Goat IgG,3723.361515151514
+15,Mouse IgG,3703.99125
+15,CD73,1577.505063291139
+15,CD107B,0.0
+15,MART1,0.0
+15,KI67,0.0
+15,pan-CK,0.0
+15,CD45,0.0
+15,ECAD,0.0
+15,aSMA,0.0
+15,CD56,0.0
+15,CD13,0.0
+15,CD63,0.0
+15,CD32,0.0
+15,CDKN1A,821.3441860465116
+15,CCNA2,0.0
+15,CDKN1C,0.0
+15,PCNA_1,0.0
+15,pAUR,0.0
+15,CDKN1B_1,0.0
+15,CCND1,0.0
+15,cPARP,0.0
+15,CDKN1B_2,0.0
+15,pCREB,0.0
+15,CCNB1,0.0
+15,CCNE,0.0
+15,PCNA_2,0.0
+15,CDK2,0.0
+15,CDKN2A,0.0

scratch

@@ -0,0 +1,6 @@
+# gates should be a dataframe where
+# Column 1 is sample_id
+# Column 2 is marker_id
+# Column 3 is gate #default just gate
+# if extra gates desired, Columns 4... are gate_1, gate_2, etc
+

src/cell_gater/model/data_model.py

@@ -7,7 +7,6 @@
 import pandas as pd
 from napari.utils.events import EmitterGroup, Event
 
-
 @dataclass
 class DataModel:
     """Model containing all necessary fields for gating."""
@@ -33,6 +32,24 @@ class DataModel:
     _gates: pd.DataFrame = field(default_factory=pd.DataFrame, init=False)
     _current_gate: float = field(default_factory=float, init=False)
 
+    @property
+    def gates(self):
+        """The gates dataframe."""
+        return self._gates
+
+    @gates.setter
+    def gates(self, gates: pd.DataFrame) -> None:
+        self._gates = gates
+
+    @property
+    def current_gate(self) -> float:
+        """The current gate value."""
+        return self._current_gate
+
+    @current_gate.setter
+    def current_gate(self, value: float) -> None:
+        self._current_gate = value
+
     def __post_init__(self) -> None:
         """Allow fields in the dataclass to emit events when changed."""
         self.events = EmitterGroup(source=self, samples=Event, regionprops_df=Event, validated=Event)

src/cell_gater/utils/misc.py

@@ -7,4 +7,4 @@
 
 def napari_notification(msg, severity=NotificationSeverity.INFO):
     notification_ = Notification(msg, severity=severity)
-    notification_manager.dispatch(notification_)
+    notification_manager.dispatch(notification_)

src/cell_gater/widgets/sample_widget.py

@@ -21,7 +21,6 @@
 from cell_gater.utils.misc import napari_notification
 from cell_gater.widgets.scatter_widget import ScatterInputWidget
 
-
 class SampleWidget(QWidget):
     """Sample widget for loading required data."""
 
@@ -53,35 +52,35 @@ def __init__(self, viewer: Viewer, model: DataModel | None = None) -> None:
         # Open sample directory dialog
         self.load_samples_button = QPushButton("Load regionprops dir")
         self.load_samples_button.clicked.connect(self._open_sample_dialog)
-        self.layout().addWidget(self.load_samples_button, 1, 0)
+        self.layout().addWidget(self.load_samples_button, 0, 1)
 
         # Open image directory dialog
         self.load_image_dir_button = QPushButton("Load image dir")
         self.load_image_dir_button.clicked.connect(self._open_image_dir_dialog)
-        self.layout().addWidget(self.load_image_dir_button, 1, 1)
+        self.layout().addWidget(self.load_image_dir_button, 0, 2)
 
         # Open mask directory dialog
         self.load_mask_dir_button = QPushButton("Load mask dir")
         self.load_mask_dir_button.clicked.connect(self._open_mask_dir_dialog)
-        self.layout().addWidget(self.load_mask_dir_button, 1, 2)
+        self.layout().addWidget(self.load_mask_dir_button, 0, 3)
 
         # The lower bound marker column dropdown
         lower_col = QLabel("Select lowerbound marker column:")
         self.lower_bound_marker_col = QComboBox()
         if len(self.model.regionprops_df) > 0:
             self.lower_bound_marker_col.addItems([None] + self.model.regionprops_df.columns)
         self.lower_bound_marker_col.currentTextChanged.connect(self._update_model_lowerbound)
-        self.layout().addWidget(lower_col, 2, 0)
-        self.layout().addWidget(self.lower_bound_marker_col, 3, 0)
+        self.layout().addWidget(lower_col, 1, 0, 1, 2)
+        self.layout().addWidget(self.lower_bound_marker_col, 1, 2, 1, 2)
 
         # The upper bound marker column dropdown
         upper_col = QLabel("Select upperbound marker column:")
         self.upper_bound_marker_col = QComboBox()
         if len(self.model.regionprops_df) > 0:
             self.upper_bound_marker_col.addItems([None] + self.model.regionprops_df.columns)
         self.upper_bound_marker_col.currentTextChanged.connect(self._update_model_upperbound)
-        self.layout().addWidget(upper_col, 2, 1)
-        self.layout().addWidget(self.upper_bound_marker_col, 3, 1)
+        self.layout().addWidget(upper_col, 2, 0, 1, 2)
+        self.layout().addWidget(self.upper_bound_marker_col, 2, 2, 1, 2)
 
         # Filter field for user to pass on strings to filter markers out.
         filter_label = QLabel("Remove markers with prefix (default: DNA,DAPI)")
@@ -90,16 +89,21 @@ def __init__(self, viewer: Viewer, model: DataModel | None = None) -> None:
             placeholderText="Prefixes separated by commas.",
         )
         self.filter_field.editingFinished.connect(self._update_filter)
-        self.layout().addWidget(filter_label, 4, 0)
-        self.layout().addWidget(self.filter_field, 5, 0)
+        self.layout().addWidget(filter_label, 3, 0, 1 ,2)
+        self.layout().addWidget(self.filter_field, 3, 3)
 
         # Button to start validating all the input
         self.validate_button = QPushButton("Validate input")
         self.validate_button.clicked.connect(self._validate)
-        self.layout().addWidget(self.validate_button, 6, 0)
+        self.layout().addWidget(self.validate_button, 4, 0, 1, 4)
 
         self.model.events.regionprops_df.connect(self._set_dropdown_marker_lowerbound)
         self.model.events.regionprops_df.connect(self._set_dropdown_marker_upperbound)
+
+        #set default bounds
+
+
+
 
     @property
     def viewer(self) -> Viewer:
@@ -176,6 +180,7 @@ def _set_dropdown_marker_lowerbound(self):
         region_props = self.model.regionprops_df
         if region_props is not None and len(region_props) > 0:
             self.lower_bound_marker_col.addItems(region_props.columns)
+        self.lower_bound_marker_col.setCurrentIndex(1) # Skip the cell id column
 
     def _set_dropdown_marker_upperbound(self):
         """Add items to dropdown menu for upperbound marker.
@@ -187,6 +192,13 @@ def _set_dropdown_marker_upperbound(self):
         region_props = self.model.regionprops_df
         if region_props is not None and len(region_props) > 0:
             self.upper_bound_marker_col.addItems(region_props.columns)
+
+        #TODO set default to column before "X_centroid"
+        # This does not work
+        # if "X_centroid" in list(self.model.regionprops_df.columns):
+        #     self.upper_bound_marker_col.setCurrentIndex(
+        #         self.model.regionprops_df.columns.index("X_centroid")-1 )
+
 
     def _update_model_lowerbound(self):
         """Update the lowerbound marker in the data model upon change of text in the lowerbound marker column widget."""