Add option to highlight certain leaves in custom plots.

CHANGELOG.md

@@ -10,9 +10,12 @@ to [Common Changelog](https://common-changelog.org)
 
 ### Changed
 
+- Improve error handling for missing input genomes and reference databases. ([#130](https://github.com/metagenlab/zDB/pull/130)) (Niklaus Johner)
+
 ### Added
 
-- Improve error handling for missing input genomes and reference databases. ([#130](https://github.com/metagenlab/zDB/pull/130)) (Niklaus Johner)
+- Add option to highlight certain leaves in custom plots. ([#131](https://github.com/metagenlab/zDB/pull/131)) (Niklaus Johner)
+
 
 ## 1.3.3 - 2024-08-08
 

webapp/chlamdb/forms.py

@@ -674,55 +674,81 @@ def get_phenotype(self):
     return GwasForm
 
 
-class CustomPlotsForm(forms.Form):
-
-    help_text = """Entry IDs can be COG, KO, Pfam, VF, AMR or orthogroups.
-    IDs should be coma separated.
-    You can add custom labels by specifying them together with the entry ID
-    separated by a colon (i.e. entryID:label)."""
-
-    entries = forms.CharField(
-        widget=forms.Textarea(attrs={'cols': 50, 'rows': 5}),
-        required=True, label="Entry IDs", help_text=help_text)
-
-    Entry = namedtuple("Entry", "id label type")
-
-    def __init__(self, db, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.db = db
-        self.helper = FormHelper()
-
-        self.helper.form_method = 'post'
-        self.helper.layout = Layout(Fieldset(
-            "",
-            Column(
-                Row(Column(
-                        "entries",
+def make_custom_plots_form():
+
+    accession_choices = AccessionFieldHandler().get_choices(
+        with_plasmids=False)
+
+    class CustomPlotsForm(forms.Form):
+
+        entries_help = """Entry IDs can be COG, KO, Pfam, VF, AMR or orthogroups.
+        IDs should be coma separated.
+        You can add custom labels by specifying them together with the entry ID
+        separated by a colon (i.e. entryID:label)."""
+
+        entries = forms.CharField(
+            widget=forms.Textarea(attrs={'cols': 50, 'rows': 5}),
+            required=True, label="Entry IDs", help_text=entries_help)
+
+        Entry = namedtuple("Entry", "id label type")
+
+        highlights_help = "Chose entries that should be highlighted in the tree."
+        highlights = forms.MultipleChoiceField(
+            choices=accession_choices,
+            widget=Select2Multiple(
+                url="autocomplete_taxid",
+                forward=(forward.Field("targets", "exclude_taxids_in_groups"),),
+                attrs={"data-close-on-select": "false",
+                       "data-placeholder": "Nothing selected"}),
+            required=False, help_text=highlights_help)
+
+        def __init__(self, db, *args, **kwargs):
+            super().__init__(*args, **kwargs)
+            self.db = db
+            self.helper = FormHelper()
+
+            self.helper.form_method = 'post'
+            self.helper.layout = Layout(Fieldset(
+                "",
+                Column(
+                    Row(Column(
+                            "entries",
+                            css_class='form-group col-lg-12 col-md-12 col-sm-12'),
+                        Column(
+                            "highlights",
+                            css_class='form-group col-lg-12 col-md-12 col-sm-12'),
+                        ),
+                    Row(Submit('submit', 'Make plot'),
                         css_class='form-group col-lg-12 col-md-12 col-sm-12'),
-                    ),
-                Row(Submit('submit', 'Make plot'),
-                    css_class='form-group col-lg-12 col-md-12 col-sm-12'),
-                css_class="col-lg-8 col-md-8 col-sm-12")
+                    css_class="col-lg-8 col-md-8 col-sm-12")
+                )
             )
-        )
 
-    def clean_entries(self):
-        raw_entries = self.cleaned_data["entries"].split(",")
-        parser = EntryIdParser(self.db)
-        entries = []
-        for entry in raw_entries:
-            entry = entry.strip()
-            if ":" in entry:
-                entry, label = entry.split(":", 1)
-            else:
-                label = entry
-            try:
-                object_type, entry_id = parser.id_to_object_type(entry)
-            except Exception:
-                raise ValidationError(f'Invalid identifier "{entry}".',
-                                      code="invalid")
-            entries.append(self.Entry(entry_id, label, object_type))
-        return entries
+        def clean_entries(self):
+            raw_entries = self.cleaned_data["entries"].split(",")
+            parser = EntryIdParser(self.db)
+            entries = []
+            for entry in raw_entries:
+                entry = entry.strip()
+                if ":" in entry:
+                    entry, label = entry.split(":", 1)
+                else:
+                    label = entry
+                try:
+                    object_type, entry_id = parser.id_to_object_type(entry)
+                except Exception:
+                    raise ValidationError(f'Invalid identifier "{entry}".',
+                                          code="invalid")
+                entries.append(self.Entry(entry_id, label, object_type))
+            return entries
+
+        def get_highlights(self):
+            indices = self.cleaned_data["highlights"]
+            taxids, plasmids = AccessionFieldHandler().extract_choices(
+                indices, False)
+            return taxids
+
+    return CustomPlotsForm
 
 
 def make_group_add_form(db):

webapp/lib/ete_phylo.py

@@ -67,7 +67,7 @@ def get_leaf_name(self, index):
             if idx in self.highlight_leaves:
                 fgcolor = "red"
         label = self.leaves_name.get(idx, self.default_val)
-        t = TextFace(label, fgcolor=fgcolor, fsize=7, fstyle="italic")
+        t = TextFace(label, fgcolor=fgcolor, fsize=7)
         t.margin_right = 13
         return t
 

webapp/views/custom_plots.py

@@ -1,4 +1,4 @@
-from chlamdb.forms import CustomPlotsForm
+from chlamdb.forms import make_custom_plots_form
 from django.conf import settings
 from django.shortcuts import render
 from django.views import View
@@ -19,7 +19,9 @@ class CusomPlotsView(View):
     template = 'chlamdb/custom_plots.html'
     _db = None
 
-    form_class = CustomPlotsForm
+    def dispatch(self, request, *args, **kwargs):
+        self.form_class = make_custom_plots_form()
+        return super(CusomPlotsView, self).dispatch(request, *args, **kwargs)
 
     def get_result_tabs(self, table):
         return [
@@ -60,6 +62,7 @@ def post(self, request, *args, **kwargs):
             return render(request, self.template, self.get_context())
 
         entries = self.form.cleaned_data["entries"]
+        to_highlight = self.form.get_highlights()
 
         # We make 1 query for each entry, although we could of course make
         # a single query for each object type, but I don't expect any
@@ -73,7 +76,7 @@ def post(self, request, *args, **kwargs):
             counts.append(hits)
 
         genome_descriptions = self.db.get_genomes_description()
-        self.prepare_tree(counts, genome_descriptions)
+        self.prepare_tree(counts, genome_descriptions, to_highlight)
         table = self.prepare_table(counts, genome_descriptions)
 
         context = self.get_context(
@@ -82,7 +85,7 @@ def post(self, request, *args, **kwargs):
             )
         return render(request, self.template, context)
 
-    def prepare_tree(self, counts_list, genome_descriptions):
+    def prepare_tree(self, counts_list, genome_descriptions, to_highlight):
         ref_tree = self.db.get_reference_phylogeny()
         ref_names = genome_descriptions.description.to_dict()
 
@@ -92,7 +95,7 @@ def prepare_tree(self, counts_list, genome_descriptions):
             tree.set_outgroup(R)
         tree.ladderize()
         e_tree = EteTree(tree)
-        e_tree.rename_leaves(ref_names)
+        e_tree.rename_leaves(ref_names, highlight_leaves=to_highlight)
         for counts in counts_list:
             for label, count in counts.iterrows():
                 col = SimpleColorColumn.fromSeries(count, header=label, color_gradient=True)