Merge pull request #108 from dengzq1234/desktop_v2

Desktop v2

Author: dengzq1234

README.md

@@ -106,8 +106,12 @@ TreeProfiler requires
   - webdriver_manager
   - pyvirtualdisplay
 
-### Quick install via pip
+### Quick Install Environment
 ```
+# create environment
+conda create -n treeprofiler python=3.10
+conda activate treeprofiler
+
 # Install ETE Toolkit v4
 pip install --force-reinstall https://github.com/etetoolkit/ete/archive/ete4.zip
 

treeprofiler/app.py

@@ -357,7 +357,6 @@ def get_array(self, node):
 
     def set_node_style(self, node):
         array = self.get_array(node)
-        #array = self.get_array(node)
         if array:
             if not self.is_list:
                 if len(self.matrix_props) > 1:
@@ -835,7 +834,7 @@ def __init__(self, seq, value2color=None,
         self.seq = seq
         self.seqlength = len(self.seq)
         self.value2color = value2color
-        self.absence_color = '#EBEBEB'
+        self.absence_color = value2color.get(None, '#EBEBEB') if value2color else '#EBEBEB'
 
         self.autoformat = True  # block if 1px contains > 1 tile
 

treeprofiler/layouts/profile_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):
@@ -302,6 +302,7 @@ def set_tree_style(self, tree, tree_style):
                                     )
     def set_node_style(self, node):
         heatmap_num = node.props.get(self.prop)
+
         if heatmap_num is not None and heatmap_num != 'NaN':
             heatmap_num = float(heatmap_num)
             if node.is_leaf:
@@ -318,7 +319,7 @@ def set_node_style(self, node):
                     color=gradient_color, padding_x=self.padding_x, padding_y=self.padding_y, tooltip=tooltip)
                     node.add_face(identF, column = self.column,  position = 'aligned')
 
-        elif node.is_leaf and node.props.get(self.internal_prop):
+        elif node.is_leaf and node.props.get(self.internal_prop) is not None:
             heatmap_num = node.props.get(self.internal_prop)
             heatmap_num = float(heatmap_num)
             # heatmap
@@ -335,7 +336,7 @@ def set_node_style(self, node):
                 color=gradient_color, padding_x=self.padding_x, padding_y=self.padding_y, tooltip=tooltip)
                 node.add_face(identF, column = self.column,  position = 'aligned', collapsed_only=True)
 
-        elif node.props.get(self.internal_prop):
+        elif node.props.get(self.internal_prop) is not None:
             heatmap_num = node.props.get(self.internal_prop)
             heatmap_num = float(heatmap_num)
             # heatmap
@@ -570,7 +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

treeprofiler/layouts/staple_layouts.py

@@ -363,7 +363,7 @@ def set_node_style(self, node):
                     tooltip += f'<br>{self.prop}: {prop_text}<br>'
 
                 if self.color_dict:
-                    color = self.color_dict.get(str(prop_text),"")
+                    color = self.color_dict.get(prop_text,"")
                     prop_face = RectFace(width=self.width, height=self.height, color=color, \
                         padding_x=self.padding_x , padding_y=self.padding_y, tooltip=tooltip)
                     node.add_face(prop_face, column=self.column, position="aligned")
@@ -458,7 +458,7 @@ def set_node_style(self, node):
                 tooltip += f'<br>{self.prop}: {prop_text}<br>'
 
             if self.color_dict:
-                color = self.color_dict.get(str(prop_text), self.absence_color)
+                color = self.color_dict.get(prop_text, self.absence_color)
                 align_link_face = AlignLinkFace(width=self.width*2, height=None,
                     stroke_color=color, stroke_width=2, line_type=0, opacity=0.7)
                 node.sm_style["bgcolor"] = color
@@ -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)
 
 

treeprofiler/layouts/text_layouts.py

@@ -13,6 +13,7 @@
 import matplotlib.colors as mcolors
 import numpy as np
 from scipy import stats
+import numbers
 import random
 import colorsys
 import operator
@@ -270,7 +271,23 @@ def get_internal_parser(internal_parser="name"):
         return 1
     elif internal_parser == "support":
         return 0
-         
+
+def get_prop2type(node):
+    output = {}
+    prop2value = node.props
+    if '_speciesFunction' in prop2value:
+        del prop2value['_speciesFunction']
+    
+    for prop, value in prop2value.items():
+        if value != 'NaN':
+            if isinstance(value, numbers.Number):
+                output[prop] = float
+            elif type(value) == list:
+                output[prop] = list
+            else:
+                output[prop] = str    
+    return output
+
 def ete4_parse(newick, internal_parser="name"):
     tree = PhyloTree(newick, parser=get_internal_parser(internal_parser))
     # Correct 0-dist trees
@@ -349,11 +366,6 @@ def conditional_prune(tree, conditions_input, prop2type):
             #         n.dist = 1
     return tree
 
-
-    #array = [n.props.get(prop) if n.props.get(prop) else 'NaN' for n in nodes] 
-    array = [n.props.get(prop) for n in nodes if n.props.get(prop) ] 
-    return array
-
 # def _tree_prop_array(node, prop, leaf_only=False, numeric=False, list_type=False):
 #     array = []
 #     sep = '||'