Merge pull request #118 from dengzq1234/desktop_v2

Desktop v2

Author: dengzq1234

treeprofiler/layouts/text_layouts.py

@@ -222,23 +222,22 @@ def set_tree_style(self, tree, tree_style):
                                     )
 
     def set_node_style(self, node):
-        if node.is_leaf and node.props.get(self.prop):
+        if node.is_leaf and node.props.get(self.prop) is not '':
             prop_text = node.props.get(self.prop)
-            if prop_text:
-                if type(prop_text) == list:
-                    prop_text = ",".join(prop_text)
-                else:
-                    pass
-                if self.color_dict:
-                    prop_face = TextFace(prop_text, color=self.color_dict.get(prop_text, 'black'),min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width )
-                else:
-                    prop_face = TextFace(prop_text, color='black', min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width )
+            if type(prop_text) == list:
+                prop_text = ",".join(prop_text)
+            else:
+                pass
+            if self.color_dict:
+                prop_face = TextFace(prop_text, color=self.color_dict.get(prop_text, 'black'),min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width )
+            else:
+                prop_face = TextFace(prop_text, color='black', min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width )
             node.add_face(prop_face, column=self.column, position="aligned")
 
         elif node.is_leaf and node.props.get(self.internal_prop):
             stackedbar_face = get_stackedbarface(node, self.internal_prop, self.color_dict, width=self.width, padding_x=self.padding_x, padding_y=self.padding_y)
             node.add_face(stackedbar_face, column = self.column, position = "aligned", collapsed_only=False)
-
+        
         elif node.props.get(self.internal_prop):
             stackedbar_face = get_stackedbarface(node, self.internal_prop, self.color_dict, width=self.width, padding_x=self.padding_x, padding_y=self.padding_y)
             node.add_face(stackedbar_face, column = self.column, position = "aligned", collapsed_only=True)
@@ -250,7 +249,67 @@ def set_node_style(self, node):
             prop_face = RectFace(width=self.width, height=self.height, color=self.absence_color, \
                     padding_x=self.padding_x , padding_y=self.padding_y, tooltip=None)
             node.add_face(prop_face, column=self.column, position="aligned", collapsed_only=True)
+            # if not node.is_leaf and node.props.get(self.prop):
+            #     prop_text = node.props.get(self.prop)
+            #     if type(prop_text) == list:
+            #         prop_text = ",".join(prop_text)
+            #     else:
+            #         pass
+            #     if self.color_dict:
+            #         prop_face = TextFace(prop_text, color=self.color_dict.get(prop_text, 'black'),min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width )
+            #     else:
+            #         prop_face = TextFace(prop_text, color='black', min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width )
+            #     node.add_face(prop_face, column=self.column, position="branch_right")
+            #     node.add_face(prop_face, column=self.column, position="branch_right", collapsed_only=True)
+
+class LayoutTextbranch(TreeLayout):
+    def __init__(self, name, column, text_color, color_dict, prop, width=70, min_fsize=5, max_fsize=15, padding_x=1, padding_y=0, legend=True, aligned_faces=True):
+        super().__init__(name, aligned_faces=aligned_faces)
+        self.aligned_faces = True
+        self.prop = prop
+        self.column = column
+        self.text_color = text_color
+        self.color_dict = color_dict
+        self.legend = legend
+        self.width = width
+        self.height = None
+        self.min_fsize = min_fsize 
+        self.max_fsize = max_fsize
+        self.padding_x = padding_x
+        self.padding_y = padding_y
 
+    def set_tree_style(self, tree, tree_style):
+        super().set_tree_style(tree, tree_style)
+        text = TextFace(self.prop, min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width, rotation=315)
+        tree_style.aligned_panel_header.add_face(text, column=self.column)
+
+        if self.legend:
+            if self.color_dict:
+                tree_style.add_legend(title=self.prop,
+                                    variable='discrete',
+                                    colormap=self.color_dict
+                                    )
+            else:
+                tree_style.add_legend(title=self.prop,
+                                    variable='discrete',
+                                    colormap={
+                                        self.prop: self.text_color
+                                        }
+                                    )
+    def set_node_style(self, node):
+        prop_text = node.props.get(self.prop)
+        if prop_text is not None and prop_text != '':
+            if type(prop_text) == list:
+                prop_text = ",".join(prop_text)
+            else:
+                pass
+            if self.text_color:
+                prop_face = TextFace(prop_text, color=self.text_color, min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width)
+            else:
+                prop_face = TextFace(prop_text, color='black', min_fsize=self.min_fsize, max_fsize=self.max_fsize, padding_x=self.padding_x, width=self.width )
+            node.add_face(prop_face, position="branch_bottom")
+            node.add_face(prop_face, position="branch_bottom", collapsed_only=True)
+   
 class LayoutColorbranch(TreeLayout):
     def __init__(self, name, column, color_dict, prop, legend=True, width=70, padding_x=1, padding_y=0):
         super().__init__(name)
@@ -540,4 +599,67 @@ def set_node_style(self, node):
                 node.add_face(prop_face, column=self.column, 
                 position="branch_right", collapsed_only=False)
 
+class LayoutSymbolbranch(TreeLayout):
+    def __init__(self, name=None, prop=None, position="branch_right",
+            column=0, symbol='circle', symbol_color=None, color_dict=None, 
+            max_radius=1, symbol_size=5, fgopacity=0.8, 
+            padding_x=2, padding_y=0, 
+            scale=True, legend=True, active=True):
 
+        name = name or f'{symbol}Branch_{prop}'
+        super().__init__(name)
+
+        self.aligned_faces = True
+        self.prop = prop
+        self.symbol = symbol # circle, square and triangle
+        self.symbol_color = symbol_color
+
+        self.column = column
+        self.position = position
+        self.color_dict = color_dict
+
+        self.max_radius = float(max_radius)
+        self.symbol_size = float(symbol_size)
+        self.fgopacity = float(fgopacity)
+
+        self.padding_x = padding_x
+        self.padding_y = padding_y
+   
+        self.legend = legend
+        self.active = active
+    
+    def set_tree_style(self, tree, tree_style):
+        super().set_tree_style(tree, tree_style)
+        if self.legend:
+            if self.color_dict and len(self.color_dict) > 1:
+                # self.color_dict['NA'] = self.absence_color
+                tree_style.add_legend(title=self.prop,
+                                    variable='discrete',
+                                    colormap=self.color_dict
+                                    )
+            else:
+                tree_style.add_legend(title=self.prop,
+                                    variable='discrete',
+                                    colormap={
+                                        self.prop: self.symbol_color
+                                        }
+                                    )
+    
+    def set_node_style(self, node):
+        prop_text = node.props.get(self.prop) 
+        if prop_text is not None and prop_text != '':
+            if type(prop_text) == list:
+                prop_text = ",".join(prop_text)
+            else:
+                pass
+            if self.color_dict and len(self.color_dict) > 1:
+                node.sm_style['shape'] = self.symbol
+                node.sm_style["fgcolor"] = self.color_dict.get(prop_text)
+                node.sm_style['size'] =  self.symbol_size
+                node.sm_style['fgopacity'] = self.fgopacity
+            else:
+                node.sm_style['shape'] = self.symbol
+                node.sm_style["fgcolor"] = self.symbol_color
+                node.sm_style['size'] =  self.symbol_size
+                node.sm_style['fgopacity'] = self.fgopacity
+

treeprofiler/tree_plot.py

@@ -206,6 +206,23 @@ def poplulate_plot_args(plot_args_p):
         nargs='+',
         required=False,
         help="<prop1> <prop2> names of properties where branches will be colored based on different values.")
+    group.add_argument('--textbranch-layout',
+        nargs='+',
+        required=False,
+        help="<prop1> <prop2> names of properties where values will be displayed on the branch in text.")
+    group.add_argument('--circlebranch-layout',
+        nargs='+',
+        required=False,
+        help="<prop1> <prop2> names of properties where values will be displayed on the branch in the shape of cricle.")
+    group.add_argument('--squarebranch-layout',
+        nargs='+',
+        required=False,
+        help="<prop1> <prop2> names of properties where values will be displayed on the branch in the shape of square.")
+    group.add_argument('--trianglebranch-layout',
+        nargs='+',
+        required=False,
+        help="<prop1> <prop2> names of properties where values will be displayed on the branch in the shape of triangle.")
+    
     group.add_argument('--label-layout',
         nargs='+',
         required=False,
@@ -537,6 +554,42 @@ def run(args):
                     visualized_props.append(prop)
                     visualized_props.append(utils.add_suffix(prop, internal_num_rep))
 
+        if layout == 'textbranch-layout':
+            textbranch_layouts, level, color_dict = get_textbranch_layouts(tree, args.textbranch_layout, 
+            level, column_width=args.column_width, prop2type=prop2type, 
+            padding_x=args.padding_x, padding_y=args.padding_y, color_config=color_config)
+            layouts.extend(textbranch_layouts)
+            for prop in args.textbranch_layout:
+                visualized_props.append(prop)
+
+        if layout == 'circlebranch-layout':
+            circlebranch_layouts, level, color_dict = get_circlebranch_layouts(tree, args.circlebranch_layout, 
+            level, prop2type=prop2type, padding_x=args.padding_x, padding_y=args.padding_y, color_config=color_config)
+            layouts.extend(circlebranch_layouts)
+            for prop in args.circlebranch_layout:
+                visualized_props.append(prop)
+
+        if layout == 'circlebranch-layout':
+            circlebranch_layouts, level, color_dict = get_circlebranch_layouts(tree, args.circlebranch_layout, 
+            level, prop2type=prop2type, padding_x=args.padding_x, padding_y=args.padding_y, color_config=color_config)
+            layouts.extend(circlebranch_layouts)
+            for prop in args.circlebranch_layout:
+                visualized_props.append(prop)
+        
+        if layout == 'squarebranch-layout':
+            squarebranch_layouts, level, color_dict = get_squarebranch_layouts(tree, args.squarebranch_layout, 
+            level, prop2type=prop2type, padding_x=args.padding_x, padding_y=args.padding_y, color_config=color_config)
+            layouts.extend(squarebranch_layouts)
+            for prop in args.squarebranch_layout:
+                visualized_props.append(prop)
+
+        if layout == 'trianglebranch-layout':
+            trianglebranch_layouts, level, color_dict = get_trianglebranch_layouts(tree, args.trianglebranch_layout, 
+            level, prop2type=prop2type, padding_x=args.padding_x, padding_y=args.padding_y, color_config=color_config)
+            layouts.extend(trianglebranch_layouts)
+            for prop in args.trianglebranch_layout:
+                visualized_props.append(prop)
+
         if layout == 'bubble-layout':
             categorical_props = [prop for prop in args.bubble_layout if prop2type.get(prop) in [str, list, bool, None]]
             if categorical_props:
@@ -1203,6 +1256,133 @@ def get_colorbranch_layouts(tree, props, level, prop2type, column_width=70, padd
         level += 1
     return layouts, level, prop_color_dict
 
+def get_textbranch_layouts(tree, props, level, prop2type, column_width=70, padding_x=1, padding_y=0, color_config=None):
+    prop_color_dict = {}
+    layouts = []
+    for prop in props:
+        color_dict = {}
+        text_color = paired_color[level]
+        if color_config and color_config.get(prop):
+            if color_config.get(prop).get('value2color'):
+                color_dict = color_config.get(prop).get('value2color')
+       
+        layout = text_layouts.LayoutTextbranch(name='TextBranch_'+prop, 
+        column=level, text_color=text_color, color_dict=color_dict, prop=prop, 
+        width=column_width, padding_x=padding_x, padding_y=padding_y)
+        layouts.append(layout)
+        level +=1 
+
+    return layouts, level, prop_color_dict
+
+def get_widthbranch_layouts(tree, props, level, prop2type, padding_x=1, padding_y=0, color_config=None):
+    return
+
+def get_circlebranch_layouts(tree, props, level, prop2type, padding_x=1, padding_y=0, color_config=None):
+    prop_color_dict = {}
+    layouts = []
+    symbol = 'circle'
+    symbol_size = 5
+    max_radius = 1
+    fgopacity = 0.8
+    
+    for prop in props:
+        color_dict = {} # key = value, value = color id
+        symbol_color = paired_color[level]
+
+        if color_config and color_config.get(prop):
+            if color_config.get(prop).get('value2color'):
+                color_dict = color_config.get(prop).get('value2color')
+        else:
+            if prop2type and prop2type.get(prop) == list:
+                leaf_values = list(map(list,set(map(tuple,utils.tree_prop_array(tree, prop)))))    
+                prop_values = [val for sublist in leaf_values for val in sublist]
+            else:
+                prop_values = sorted(list(set(utils.tree_prop_array(tree, prop))))
+            
+            # normal text prop
+            color_dict = utils.assign_color_to_values(prop_values, paired_color)
+
+        layout = text_layouts.LayoutSymbolbranch(f'{symbol}Branch_{prop}', prop=prop,
+            column=level, symbol=symbol, symbol_color=symbol_color, color_dict=color_dict,
+            max_radius=max_radius, symbol_size=symbol_size, 
+            padding_x=padding_x, padding_y=padding_y, fgopacity=fgopacity,
+            scale=True, legend=True, active=True
+            )
+        layouts.append(layout)
+        level +=1 
+    
+    return layouts, level, prop_color_dict
+
+def get_squarebranch_layouts(tree, props, level, prop2type, padding_x=1, padding_y=0, color_config=None):
+    prop_color_dict = {}
+    layouts = []
+    symbol = 'square'
+    symbol_size = 5
+    max_radius = 1
+    fgopacity = 0.8
+    
+    for prop in props:
+        color_dict = {} # key = value, value = color id
+        symbol_color = paired_color[level]
+
+        if color_config and color_config.get(prop):
+            if color_config.get(prop).get('value2color'):
+                color_dict = color_config.get(prop).get('value2color')
+        else:
+            if prop2type and prop2type.get(prop) == list:
+                leaf_values = list(map(list,set(map(tuple,utils.tree_prop_array(tree, prop)))))    
+                prop_values = [val for sublist in leaf_values for val in sublist]
+            else:
+                prop_values = sorted(list(set(utils.tree_prop_array(tree, prop))))
+            
+            # normal text prop
+            color_dict = utils.assign_color_to_values(prop_values, paired_color)
+
+        layout = text_layouts.LayoutSymbolbranch(f'{symbol}Branch_{prop}', prop=prop,
+            column=level, symbol=symbol, symbol_color=symbol_color, color_dict=color_dict,
+            max_radius=max_radius, symbol_size=symbol_size, 
+            padding_x=padding_x, padding_y=padding_y, fgopacity=fgopacity,
+            scale=True, legend=True, active=True
+            )
+        layouts.append(layout)
+        level +=1 
+    return layouts, level, prop_color_dict
+
+def get_trianglebranch_layouts(tree, props, level, prop2type, padding_x=1, padding_y=0, color_config=None):
+    prop_color_dict = {}
+    layouts = []
+    symbol = 'triangle'
+    symbol_size = 5
+    max_radius = 1
+    fgopacity = 0.8
+    
+    for prop in props:
+        color_dict = {} # key = value, value = color id
+        symbol_color = paired_color[level]
+
+        if color_config and color_config.get(prop):
+            if color_config.get(prop).get('value2color'):
+                color_dict = color_config.get(prop).get('value2color')
+        else:
+            if prop2type and prop2type.get(prop) == list:
+                leaf_values = list(map(list,set(map(tuple,utils.tree_prop_array(tree, prop)))))    
+                prop_values = [val for sublist in leaf_values for val in sublist]
+            else:
+                prop_values = sorted(list(set(utils.tree_prop_array(tree, prop))))
+            
+            # normal text prop
+            color_dict = utils.assign_color_to_values(prop_values, paired_color)
+
+        layout = text_layouts.LayoutSymbolbranch(f'{symbol}Branch_{prop}', prop=prop,
+            column=level, symbol=symbol, symbol_color=symbol_color, color_dict=color_dict,
+            max_radius=max_radius, symbol_size=symbol_size, 
+            padding_x=padding_x, padding_y=padding_y, fgopacity=fgopacity,
+            scale=True, legend=True, active=True
+            )
+        layouts.append(layout)
+        level +=1 
+    return layouts, level, prop_color_dict
+
 def get_rectangle_layouts(tree, props, level, prop2type, column_width=70, padding_x=1, padding_y=0, color_config=None, precomputed_props={}):
     prop_color_dict = {}
     layouts = []

treeprofiler/views/upload_tree.html

@@ -355,8 +355,6 @@ <h5>Pfam Annotation from emapper (Optional)</h5>
             </div>
         </div>
 
-        
-
         <!-- Submit Button -->
         <button type="button" class="btn btn-primary" onclick="submitForm()">Annotate and Visualize Tree!</button>
     </form>