issue #1104 - Samples per variant - option to hide ref variants

SACGF · Dec 6, 2024 · 494261c · 494261c
1 parent a00a696
commit 494261c
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Showing 3 changed files with 48 additions and 7 deletions.
diff --git a/snpdb/variant_sample_information.py b/snpdb/variant_sample_information.py
@@ -28,18 +28,16 @@ def __init__(self, user, variant, genome_build: GenomeBuild):
         visible_samples_qs = Sample.filter_for_user(user).filter(vcf__genome_build=self.genome_build)
         self.user_sample_ids = set(visible_samples_qs.values_list("pk", flat=True))
         self.num_user_samples = len(self.user_sample_ids)
+        self.visible_zygosity_counts = Counter()
 
         locus_counter = defaultdict(Counter)
         locus_patients = defaultdict(set)
         num_observations = 0
         self.visible_rows = []
         for row in values_qs:
             pk = row["variant"]
-            if zygosity := row.get("zygosity"):
-                locus_counter[pk][zygosity] += 1
-            else:
-                locus_counter[pk][Zygosity.UNKNOWN_ZYGOSITY] += 0  # Need an entry to make it show...
-
+            zygosity = row.get("zygosity", Zygosity.UNKNOWN_ZYGOSITY)
+            locus_counter[pk][zygosity] += 1
             if patient := row.get("sample__patient"):
                 locus_patients[pk].add(patient)
 
@@ -49,6 +47,7 @@ def __init__(self, user, variant, genome_build: GenomeBuild):
 
                     if sample_id in self.user_sample_ids:
                         self.visible_rows.append(row)
+                        self.visible_zygosity_counts[zygosity] += 1
 
         has_hidden_samples = self.num_samples > self.num_user_samples
         self.hidden_samples_details = {}

diff --git a/variantopedia/templates/variantopedia/variant_sample_information.html b/variantopedia/templates/variantopedia/variant_sample_information.html
@@ -99,6 +99,13 @@ <h3>Samples</h3>
 	{% if not vsi.hidden_samples_details or vsi.hidden_samples_details.num_visible_observations %}
 
 	   <div id="genotype-grid-container">
+            <form id="genotype-grid-form">
+                <label>Ref ({{ vsi.visible_zygosity_counts.R }}):</label> <input checked type="checkbox" class="genotype-filter" data-field="zygosity" value="R"> <span class="separator">|</span>
+                <label>HET ({{ vsi.visible_zygosity_counts.E }}):</label> <input checked type="checkbox" class="genotype-filter" data-field="zygosity" value="E"> <span class="separator">|</span>
+                <label>HOM ({{ vsi.visible_zygosity_counts.O }}):</label> <input checked type="checkbox" class="genotype-filter" data-field="zygosity" value="O"> <span class="separator">|</span>
+                <label>unknown/? ({{ vsi.visible_zygosity_counts.U }}):</label> <input checked type="checkbox" class="genotype-filter" data-field="zygosity" value="U">
+            </form>
+
            <table id="genotype-grid"></table>	       
            <div id="genotype-grid-pager"></div> 
 	   </div>
@@ -191,9 +198,39 @@ <h3>Samples</h3>
 
         }
 
+        function filterGenotypes() {
+            let genotypes = [];
+            console.log("filterGenotypes")
+            $(".genotype-filter").each(function() {
+                if ($(this).is(":checked")) {
+                    genotypes.push($(this).attr("value"));
+                }
+            });
+            console.log(genotypes);
+
+            const filters = {
+                groupOp: "OR", // Match any of the conditions
+                rules: [
+                        {
+                            field: "zygosity",
+                            op: "in",
+                            data: genotypes
+                        }
+                ]
+            };
+
+            $("#genotype-grid").jqGrid("setGridParam", {
+                search: true,
+                postData: {
+                    filters: JSON.stringify(filters)
+                }
+            }).trigger("reloadGrid");
+
+        }
+
 
         $(document).ready(function() {
-            const visible_rows = {{ visible_rows | jsonify }};
+            const visible_rows = {{ vsi.visible_rows | jsonify }};
             const ZYGOSITY_DICT = {
                 'O': 'HOM_ALT',
                 'E': 'HET',
@@ -243,6 +280,8 @@ <h3>Samples</h3>
                 pager: 'genotype-grid-pager',
             });
 
+            $(".genotype-filter").change(filterGenotypes);
+
             plotSampleAlleleFrequencies(visible_rows);
         });
 
@@ -273,6 +312,10 @@ <h3>Phenotypes/OMIM</h3>
     td.no-word-wrap {
         white-space: normal !important;
     }
+
+    .separator {
+        padding: 0 5 0 5;
+    }
     </style>
 
     {% load patient_graph_tags %}

diff --git a/variantopedia/views.py b/variantopedia/views.py
@@ -640,7 +640,6 @@ def variant_sample_information(request, variant_id, genome_build_name):
     context = {
         "variant": variant,
         "vsi": vsi,
-        "visible_rows": vsi.visible_rows,
         "other_loci_variants_by_multiallelic": other_loci_variants_by_multiallelic,
         "has_samples_in_other_builds": Sample.objects.exclude(vcf__genome_build=genome_build).exists(),
     }