Merge pull request #52 from dengzq1234/main

set ls layout as manual activate

treeprofiler/layouts/phylosignal_layouts.py

@@ -116,7 +116,7 @@ def __init__(self, name, ls_prop, color, legend=True):
         self.ls_prop = ls_prop
         self.color = color
         self.legend = legend
-
+        self.active = False
     def set_tree_style(self, tree, tree_style):
         if self.legend:
 

treeprofiler/layouts/staple_layouts.py

@@ -358,6 +358,7 @@ def __init__(self, name, color_dict, score_prop, internal_rep=None, \
         self.color_range = color_range
         self.show_score = show_score
         self.line_width = 3
+        self.active = False
 
     def set_tree_style(self, tree, tree_style):
         if self.legend:

treeprofiler/layouts/taxon_layouts.py

@@ -230,9 +230,12 @@ def set_node_style(self, node):
                 lca_face = RectFace(self.rect_width, None, text = lca, color=color, padding_x=1, padding_y=1, tooltip=tooltip)
                 lca_face.rotate_text = True
                 node.sm_style["draw_descendants"] = False
+
                 node.add_face(lca_face, position='aligned', column=level)
                 node.add_face(lca_face, position='aligned', column=level,
                     collapsed_only=True)
+                node.add_face(TextFace(lca, color = color, padding_x=2),
+                column=1, position="branch_right", collapsed_only=True)
 
             # elif node_sciname and (node_rank == self.rank):
             #     lca = node_sciname

treeprofiler/tree_annotate.py

@@ -1385,11 +1385,13 @@ def annot_tree_pfam_table(post_tree, pfam_table, alg_fasta, domain_prop='dom_arq
                 dom_start = int(info[7])
                 dom_end = int(info[8])
                 if raw2alg.get(seq_name):
-                    trans_dom_start = raw2alg[seq_name][dom_start]
-                    trans_dom_end = raw2alg[seq_name][dom_end]
-                    dom_info_string = pair_delimiter.join([dom_name, str(trans_dom_start), str(trans_dom_end)])
-                    seq2doms[seq_name].append(dom_info_string)
-
+                    try:
+                        trans_dom_start = raw2alg[seq_name][dom_start]
+                        trans_dom_end = raw2alg[seq_name][dom_end]
+                        dom_info_string = pair_delimiter.join([dom_name, str(trans_dom_start), str(trans_dom_end)])
+                        seq2doms[seq_name].append(dom_info_string)
+                    except KeyError:
+                        raise KeyError(f"Cannot find {dom_start} or {dom_end} in {seq_name}")
     for l in post_tree:
         if l.name in seq2doms.keys():
             domains = seq2doms[l.name]

treeprofiler/tree_plot.py

@@ -494,11 +494,15 @@ def run(args):
             if not rank2values:
                 rank2values = defaultdict(list)
                 for n in tree.traverse():
-                    if n.props.get('rank') and n.props.get('rank') != 'Unknown':
-                        rank2values[n.props.get('rank')].append(n.props.get('sci_name',''))
+                    if n.props.get('lca'):
+                        for rank, sci_name in n.props.get('lca').items():
+                            rank2values[rank].append(sci_name)
+
+                    current_rank = n.props.get('rank')
+                    if current_rank and current_rank != 'Unknown':
+                        rank2values[current_rank].append(n.props.get('sci_name',''))
             else:       
                 pass
-
 
             # assign color for each value of each rank
             for rank, value in sorted(rank2values.items()):
@@ -590,9 +594,9 @@ def run(args):
                 taxa_layouts.append(taxa_layout)
                 #level += 1
 
-            if args.taxoncollapse_layout:
-                taxa_layout = taxon_layouts.TaxaCollapse(name = "TaxaCollapse_"+rank, rank=rank, rect_width=args.column_width, color_dict=color_dict, column=level)
-                taxa_layouts.append(taxa_layout)
+            # if args.taxoncollapse_layout:
+            #     taxa_layout = taxon_layouts.TaxaCollapse(name = "TaxaCollapse_"+rank, rank=rank, rect_width=args.column_width, color_dict=color_dict, column=level)
+            #     taxa_layouts.append(taxa_layout)
 
             taxon_color_dict[rank] = color_dict