update alignment width, midgroup

Author: dengzq1234

treeprofiler/layouts/seq_layouts.py

@@ -21,13 +21,13 @@ def get_colormap():
 
 class LayoutAlignment(TreeLayout):
     def __init__(self, name="Alignment",
-            alignment=None, alignment_prop=None, format='seq', width=700, height=15,
+            alignment=None, alignment_prop=None, format='seq', width=800, height=15,
             column=0, scale_range=None, window=[], summarize_inner_nodes=True, 
             aligned_faces=True):
         super().__init__(name, aligned_faces=aligned_faces)
         #self.alignment = SeqGroup(alignment) if alignment else None
         self.alignment_prop = alignment_prop
-        self.width = width
+        self.width = int(width)
         self.height = height
         self.column = column
         self.aligned_faces = True
@@ -81,20 +81,30 @@ def layout_fn(node):
 class LayoutDomain(TreeLayout):
     def __init__(self, prop, name,
             column=10, colormap={},
-            min_fsize=4, max_fsize=15,
-            padding_x=5, padding_y=0):
+            min_fsize=4, max_fsize=15, 
+            padding_x=5, padding_y=0, width=800):
         super().__init__(name or "Domains layout")
         self.prop = prop
         self.column = column
         self.aligned_faces = True
         self.min_fsize = min_fsize
         self.max_fsize = max_fsize
         self.padding = draw_helpers.Padding(padding_x, padding_y)
+        self.width = int(width)
         if not colormap:
             self.colormap = get_colormap()
         else:
             self.colormap = colormap
 
+    def set_tree_style(self, tree, tree_style):
+        super().set_tree_style(tree, tree_style)
+        if self.legend:
+            if self.colormap:
+                tree_style.add_legend(title=self.name,
+                                    variable='discrete',
+                                    colormap=self.colormap,
+                                    )
+
     def get_doms(self, node):
         pair_delimiter = "@"
         item_seperator = "||"
@@ -118,7 +128,7 @@ def parse_doms(self, dom_list):
             color = self.colormap.get(name, "lightgray")
             dom = [int(start), int(end), "()", 
                    None, None, color, color,
-                   "arial|30|black|%s" %(name)]
+                   f"arial|30|black|{name}"]
             doms.append(dom)
         return doms
 
@@ -129,13 +139,13 @@ def set_node_style(self, node):
             fake_seq = '-' * int(node.props.get("len_alg", 0))
 
             if doms or fake_seq:
-                seqFace = SeqMotifFace(seq=fake_seq, motifs=doms, width=400,
+                seqFace = SeqMotifFace(seq=fake_seq, motifs=doms, width=self.width,
                         height=30)
                 node.add_face(seqFace, column=self.column, 
                         position="aligned",
                         collapsed_only=(not node.is_leaf))
-        else:
-            print("no domain found for node %s" % node.name)
+        # else:
+        #     print("no domain found for node %s" % node.name)
 
 class ScaleFace(Face):
     def __init__(self, name='', width=None, color='black',

treeprofiler/main.py

@@ -48,6 +48,11 @@ def populate_main_args(main_args_p):
         action='store_true',
         required=False,
         help="Preprocess tree by changing polytomies into series of dicotomies.")
+    group.add_argument('--midgroup',
+        default=False,
+        action='store_true',
+        required=False,
+        help="Set midgroup for the tree, which is used to determine the root of the tree. ")
     group = main_args_p.add_argument_group(title='Pruning parameters',
         description="Auto pruning parameters")
     group.add_argument('--rank-limit',

treeprofiler/tree_annotate.py

@@ -775,6 +775,9 @@ def run(args):
     if args.resolve_polytomy:
         tree.resolve_polytomy()
 
+    if args.midgroup:
+        tree.set_outgroup(tree.get_midpoint_outgroup())
+        
     # set logger level
     if args.quiet:
         logger.setLevel(logging.CRITICAL)  # Mute all log levels below CRITICA
@@ -1400,8 +1403,9 @@ def process_node(node_data):
     if alignment and name2seq is not None:  # Check alignment and name2seq together
         aln_sum = column2method.get('alignment')
         if aln_sum is None or aln_sum != 'none' or consensus_cutoff is not None:
-            matrix_string = build_matrix_string(node, name2seq)  # Assuming 'name2seq' is accessible here
-            consensus_seq = utils.get_consensus_seq(matrix_string, threshold=consensus_cutoff)
+            if consensus_cutoff != 0:
+                matrix_string = build_matrix_string(node, name2seq)  # Assuming 'name2seq' is accessible here
+                consensus_seq = utils.get_consensus_seq(matrix_string, threshold=consensus_cutoff)
 
     return internal_props, consensus_seq
 

treeprofiler/tree_plot.py

@@ -302,6 +302,10 @@ def poplulate_plot_args(plot_args_p):
         default=None,
         required=False,
         help="Set the window of alignment layout. Such as: 3-200, from position 3 to 200.")
+    group.add_argument('--alignment-width',
+        default=800,
+        required=False,
+        help="Set the width of alignment/domain layout, default is 800px.")
     group.add_argument('--profiling-layout',
         nargs='+',
         required=False,
@@ -394,6 +398,9 @@ def run(args):
     if args.resolve_polytomy:
         tree.resolve_polytomy()
 
+    if args.midgroup:
+        tree.set_outgroup(tree.get_midpoint_outgroup())
+
     #rest_prop = []
     if args.prop2type:
         if eteformat_flag:
@@ -715,13 +722,15 @@ def run(args):
             else:
                 window = []
 
+            width = args.alignment_width 
             aln_layout = seq_layouts.LayoutAlignment(name='Alignment', 
                         alignment_prop='alignment', column=level, scale_range=lengh, 
-                        window=window, summarize_inner_nodes=True)
+                        window=window, width=width, summarize_inner_nodes=True)
             layouts.append(aln_layout)
 
         if layout == 'domain-layout':
-            domain_layout = seq_layouts.LayoutDomain(name="Domain", prop='dom_arq')
+            width = args.alignment_width 
+            domain_layout = seq_layouts.LayoutDomain(name="Domain", prop='dom_arq', width=width)
             layouts.append(domain_layout)
 
         # presence-absence profiling based on categorical data