handling of whitespace in guide table added...

scgv/models/loader.py

@@ -37,7 +37,7 @@ def load(self):
         self.ratio_df = self.data.get('ratio', None)
         self.clone_df = self.data.get('clone', None)
         self.tree_df = self.data.get('tree', None)
-        self.guide_df = self.data.get('guide', None)
+        self.guide_df = self._guide_clenup(self.data.get('guide', None))
         self.featuremat_df = self.data.get('featuremat', None)
         self.features_df = self.data.get('features', None)
         self.genome = self.data.get('genome', 'hg19')
@@ -46,6 +46,13 @@ def load(self):
         assert self.seg_df is not None
         assert self.genome is not None
 
+    def _guide_clenup(self, guide_df):
+        if guide_df is None:
+            return None
+        for column in guide_df.select_dtypes(include=[object]).columns:
+            guide_df[column] = guide_df[column].str.strip()
+        return guide_df
+
     @classmethod
     def _organize_filenames(cls, namelist):
         print(namelist)

scgv/models/model.py

@@ -274,8 +274,6 @@ def make_sectors_legend(self):
             return None
 
         sectors, sector_mapping = self.make_sector(self.ordering)
-        print(sector_mapping)
-
         pathology_mapping = {}
         for sector_key, sector_value in sector_mapping.items():
             sector_df = self.data.guide_df[
@@ -290,7 +288,11 @@ def make_sectors_legend(self):
                           .format(
                                 sector_key,
                                 sector_df[self.PATHOLOGY_COLUMN].unique()))
-            pathology_mapping[str(pathology).strip()] = sector_value
+
+            pathology = str(pathology).strip()
+            assert pathology not in pathology_mapping
+
+            pathology_mapping[pathology] = sector_value
         return sectors, pathology_mapping
 
 

scgv/qtviews/heatmap.py

@@ -139,10 +139,9 @@ def show(self):
         vmin = min(self.mapping.values())
 
         self.legend.clear()
-        print(self.mapping)
-
         for key, value in self.mapping.items():
-            color = self.cmap.colors[int(value) - vmin]
+            index = int(value) - vmin
+            color = self.cmap.colors[index]
             self.legend.add_entry(
                 text=str(key),
                 color=color)
@@ -257,7 +256,7 @@ def set_model(self, model):
 
         self.legend.set_model(model)
         self.model = model
-        self.tracks = self.model.tracks        
+        self.tracks = self.model.tracks
         self.selected_track = None
         if not self.tracks:
             return

scgv/views/track.py

@@ -13,16 +13,13 @@ def select_colormap(self, track_mapping):
 
         assert size <= 20
         if size > 12:
-            print("select_colormap: tab20")
             cmap = plt.get_cmap('tab20')
         elif size > 7:
-            print("select_colormap: Paired")
             cmap = plt.get_cmap('Paired')
         else:
-            print("select_colormap: tab10")
             cmap = plt.get_cmap('tab10')
-
-        return ListedColormap(cmap.colors[:size])
+        colors = cmap.colors[:size]
+        return ListedColormap(colors)
 
     def __init__(self, model, track_name, track, mapping):
         super(TrackViewer, self).__init__(model)