Merge pull request #109 from compgenomicslab/dev-repo

Dev repo
compgenomicslab · Jan 14, 2025 · 221b335 · 221b335
2 parents 7f593bc + 75ba902
commit 221b335
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Showing 6 changed files with 1,016 additions and 201 deletions.
diff --git a/treeprofiler/app.py b/treeprofiler/app.py
diff --git a/treeprofiler/layouts/staple_layouts.py b/treeprofiler/layouts/staple_layouts.py
@@ -70,7 +70,6 @@ def __init__(self, name=None, prop=None, width=200, size_prop=None,
         self.size_prop = size_prop
         self.color_prop = color_prop
         self.size_range = size_range
-        self.size_range = size_range
 
         self.color = color
         self.colors = colors
@@ -145,6 +144,7 @@ def get_size(self, node, prop):
         if not self.size_prop:
             return self.width
         minval, maxval = self.size_range
+
         return float(node.props.get(prop, 0)) / maxval * self.width
 
     def get_color(self, node):
@@ -571,7 +571,7 @@ def __init__(self, name=None, prop=None, position="aligned",
             bubble_range=[], color_range=[], internal_rep='avg',
             scale=True, legend=True, active=True):
 
-        name = name or f'Bubble_{prop}'
+        name = name or f'NumericalBubble_{prop}'
         super().__init__(name)
 
         self.aligned_faces = True

diff --git a/treeprofiler/layouts/text_layouts.py b/treeprofiler/layouts/text_layouts.py
@@ -487,7 +487,7 @@ def __init__(self, name=None, prop=None, position="branch_right",
             max_radius=1, padding_x=2, padding_y=0, 
             scale=True, legend=True, active=True):
 
-        name = name or f'Bubble_{prop}'
+        name = name or f'CategoricalBubble_{prop}'
         super().__init__(name)
 
         self.aligned_faces = True
@@ -537,7 +537,7 @@ def set_node_style(self, node):
                 # node.sm_style["fgopacity"] = self.fgopacity
                 prop_face = CircleFace(radius=bubble_size, color=bubble_color, 
                 padding_x=self.padding_x, padding_y=self.padding_y)
-                node.add_face(prop_face, column=0, 
+                node.add_face(prop_face, column=self.column, 
                 position="branch_right", collapsed_only=False)
 
 
diff --git a/treeprofiler/tree_plot.py b/treeprofiler/tree_plot.py
@@ -480,21 +480,30 @@ def run(args):
         #     layouts.extend(heatmap_layouts)
 
         if layout == 'heatmap-layout':
-            heatmap_layouts, level = get_heatmap_layouts(tree, args.heatmap_layout, level, column_width=args.column_width, padding_x=args.padding_x, padding_y=args.padding_y, internal_rep=internal_num_rep, color_config=color_config, norm_method='min-max')
+            heatmap_layouts, level = get_heatmap_layouts(tree, 
+            args.heatmap_layout, level, column_width=args.column_width, 
+            padding_x=args.padding_x, padding_y=args.padding_y, 
+            internal_rep=internal_num_rep, color_config=color_config, norm_method='min-max')
             layouts.extend(heatmap_layouts)
             for prop in args.heatmap_layout:
                 visualized_props.append(prop)
                 visualized_props.append(utils.add_suffix(prop, internal_num_rep))
 
         if layout == 'heatmap-mean-layout':
-            heatmap_mean_layouts, level = get_heatmap_layouts(tree, args.heatmap_mean_layout, level, column_width=args.column_width, padding_x=args.padding_x, padding_y=args.padding_y, internal_rep=internal_num_rep, color_config=color_config, norm_method='mean')
+            heatmap_mean_layouts, level = get_heatmap_layouts(tree, 
+            args.heatmap_mean_layout, level, column_width=args.column_width, 
+            padding_x=args.padding_x, padding_y=args.padding_y, 
+            internal_rep=internal_num_rep, color_config=color_config, norm_method='mean')
             layouts.extend(heatmap_mean_layouts)
             for prop in args.heatmap_mean_layout:
                 visualized_props.append(prop)
                 visualized_props.append(utils.add_suffix(prop, internal_num_rep))
 
         if layout == 'heatmap-zscore-layout':
-            heatmap_zscore_layouts, level = get_heatmap_layouts(tree, args.heatmap_zscore_layout, level, column_width=args.column_width, padding_x=args.padding_x, padding_y=args.padding_y, internal_rep=internal_num_rep, color_config=color_config, norm_method='zscore')
+            heatmap_zscore_layouts, level = get_heatmap_layouts(tree, 
+            args.heatmap_zscore_layout, level, column_width=args.column_width, 
+            padding_x=args.padding_x, padding_y=args.padding_y, 
+            internal_rep=internal_num_rep, color_config=color_config, norm_method='zscore')
             layouts.extend(heatmap_zscore_layouts)
             for prop in args.heatmap_zscore_layout:
                 visualized_props.append(prop)
@@ -1499,6 +1508,7 @@ def get_categorical_bubble_layouts(tree, props, level, prop2type, column_width=7
     prop_color_dict = {}
     layouts = []
     max_radius = 15
+    level = level + 1 # add one more level for bubble layout because 0 is leaf name
     for prop in props:
         color_dict = {} # key = value, value = color id
         if color_config and color_config.get(prop):
@@ -1518,11 +1528,7 @@ def get_categorical_bubble_layouts(tree, props, level, prop2type, column_width=7
             # normal text prop
             color_dict = utils.assign_color_to_values(prop_values, paired_color)
 
-        # layout = text_layouts.LayoutRect(name='Rectangular_'+prop, column=level,
-        #             color_dict=color_dict, prop=prop,
-        #             width=column_width, padding_x=padding_x, padding_y=padding_y)
-        # Configure and add layout
-        layout = text_layouts.LayoutBubbleCategorical(name=f'Bubble_{prop}', column=level, 
+        layout = text_layouts.LayoutBubbleCategorical(name=f'Categorical-Bubble_{prop}', column=level, 
         prop=prop, color_dict=color_dict, 
         max_radius=max_radius, padding_x=padding_x, padding_y=padding_y)
 
@@ -1606,7 +1612,7 @@ def process_prop_values(tree, prop):
                 value2color[val] = gradientscolor[color_index+1]
 
         # Configure and add layout
-        layout = staple_layouts.LayoutBubbleNumerical(name=f'Bubble_{prop}', 
+        layout = staple_layouts.LayoutBubbleNumerical(name=f'Numerical-Bubble_{prop}', 
         column=level, prop=prop, max_radius=max_radius, abs_maxval=abs_maxval, 
         padding_x=padding_x, padding_y=padding_y, value2color=value2color, 
         bubble_range=bubble_range,