Merge pull request #107 from dengzq1234/desktop_v2

Desktop v2
compgenomicslab · Dec 18, 2024 · 7f593bc · 7f593bc
2 parents ff084c5 + 06f833e
commit 7f593bc
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Showing 3 changed files with 19 additions and 23 deletions.
diff --git a/treeprofiler/layouts/profile_layouts.py b/treeprofiler/layouts/profile_layouts.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:

diff --git a/treeprofiler/tree_annotate.py b/treeprofiler/tree_annotate.py
@@ -39,6 +39,8 @@
                 'dup_sp': str,
                 'dup_percent': float,
                 'lca': str,
+                'common_name': str,
+                'species': str,
                 }
 
 # Global Variable for emapper headers
@@ -269,7 +271,7 @@ def run_tree_annotate(tree, input_annotated_tree=False,
     total_color_dict = []
     layouts = []
     level = 1 # level 1 is the leaf name
-    taxa_props = ['rank', 'sci_name', 'taxid', 'lineage', 'named_lineage', 'lca', 'evoltype', 'common_name', 'species']
+
     if text_prop:
         text_prop = text_prop
     else:
@@ -352,12 +354,12 @@ def run_tree_annotate(tree, input_annotated_tree=False,
 
                 else:
                     if dtype == list:
-                        multiple_text_prop.append(key)
+                        if key not in TAXONOMICDICT.keys():
+                            multiple_text_prop.append(key)
                     if dtype == str:
-                        if key not in multiple_text_prop and key not in taxa_props:
+                        if key not in multiple_text_prop and key not in TAXONOMICDICT.keys():
                             text_prop.append(key)
-                        else:
-                            pass
+
                     if dtype == float:
                         num_prop.append(key)
                     if dtype == bool:
@@ -736,6 +738,8 @@ def run(args):
             prop2type.update(utils.get_prop2type(node))
         del prop2type['name']
         del prop2type['dist']
+        if '__id' in prop2type:
+            del prop2type['__id']
         if 'support' in prop2type:
             del prop2type['support']
 
@@ -1380,7 +1384,6 @@ def merge_text_annotations(nodes, target_props, column2method, emapper_mode=Fals
     for target_prop in target_props:
         counter_stat = column2method.get(target_prop, "raw")
         prop_list = utils.children_prop_array_missing(nodes, target_prop)
-
         counter = dict(Counter(prop_list))  # Store the counter
         if 'NaN' in counter:
             del counter['NaN']

diff --git a/treeprofiler/tree_plot.py b/treeprofiler/tree_plot.py
@@ -689,7 +689,7 @@ def run(args):
             matrix, minval, maxval, value2color, results_list, list_props, single_props = numerical2matrix(tree, 
                 numerical_props, count_negative=True, internal_num_rep=internal_num_rep, 
                 color_config=color_config, norm_method='min-max')
-            
+
             if list_props:
                 index_map = {value: idx for idx, value in enumerate(numerical_props)}
                 sorted_list_props = sorted(list_props, key=lambda x: index_map[x])
@@ -1990,23 +1990,17 @@ def process_color_configuration(node2matrix, profiling_props=None):
     for node in tree.traverse():
         node2matrix_single[node.name] = []
         for profiling_prop in profiling_props:
-            if node.is_leaf:
-                prop_value = node.props.get(profiling_prop)
-                if prop_value is not None:
-                    if isinstance(prop_value, list):
-                        list_props.add(profiling_prop)
-                        prop_value = list(map(float, prop_value))
-                        if node.name not in node2matrix_list[profiling_prop]:
-                            node2matrix_list[profiling_prop][node.name] = []
-                        node2matrix_list[profiling_prop][node.name] = prop_value
-                    else:
-                        single_props.add(profiling_prop)
-                        node2matrix_single[node.name].append(float(prop_value))
-                else:
-                    node2matrix_single[node.name].append(None)
+            prop_value = node.props.get(profiling_prop)
+            if prop_value is not None:
+                if isinstance(prop_value, list):
+                    list_props.add(profiling_prop)
+                    prop_value = list(map(float, prop_value))
                     if node.name not in node2matrix_list[profiling_prop]:
                         node2matrix_list[profiling_prop][node.name] = []
-                    node2matrix_list[profiling_prop][node.name].append(None)
+                    node2matrix_list[profiling_prop][node.name] = prop_value
+                else:
+                    single_props.add(profiling_prop)
+                    node2matrix_single[node.name].append(float(prop_value))
             else:
                 if internal_num_rep != 'none':
                     representative_prop = utils.add_suffix(profiling_prop, internal_num_rep)