G3 540 genes in threshold

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.5.6"
+version = "1.5.7"
 description = ""
 authors = ["Alexander Berger <[email protected]>"]
 readme = "README.md"

src/application.py

@@ -2005,6 +2005,8 @@ def render_set_threshold(gs_id):
     if threshold_type == 1 or threshold_type == 2:
         threshold_gene_counts = calc_genes_count_in_threshold(gsv_values, thresh)
         curr_gene_count = curr_gene_count if thresh[0] == 'None' else threshold_gene_counts[float(thresh[0])]
+    elif threshold_type == 4 or threshold_type == 5:
+        curr_gene_count = calc_genes_in_threshold_range(gsv_values, thresh[0], thresh[1])
 
     score_types = {
         1: "p-value",
@@ -2045,7 +2047,28 @@ def calc_genes_count_in_threshold(gsv_values, curr_thresh) -> dict:
 
     return threshold_gene_counts
 
+def calc_genes_in_threshold_range(gsv_values, min_thresh, max_thresh) -> int:
+    """ Calculate the number of genes that fall within a given threshold range
 
+    :param gsv_values: list of gene set values
+    :param min_thresh: minimum threshold value
+    :param max_thresh: maximum threshold value
+    :return: number of genes that fall within the threshold range
+    """
+    if min_thresh is None or max_thresh == '0':
+        return 0
+
+    min_thresh = float(min_thresh)
+    max_thresh = float(max_thresh)
+
+    gene_count = 0
+    if gsv_values is not None:
+        for gsv_value in gsv_values:
+            value = list(gsv_value.values())[0]
+            if min_thresh <= float(value) <= max_thresh:
+                gene_count += 1
+
+    return gene_count
 
 @app.route('/setthreshold-legacy/<int:gs_id>')
 def render_set_threshold_legacy(gs_id):
@@ -2777,6 +2800,21 @@ def render_viewgeneset_main(gs_id, curation_view=None, curation_team=None, curat
             if plat['pf_id'] == gene_type:
                 uploaded_as = plat['pf_name']
 
+    threshold = str(geneset.threshold)
+    threshold_type = geneset.threshold_type
+    curr_threshold = threshold.split(',')
+
+    gsv_values = geneweaverdb.get_all_geneset_values(gs_id)
+    # get genes count for the current threshold
+    num_genes_in_threshold = 0;
+    if threshold_type == 1 or threshold_type == 2:
+        gene_counts = calc_genes_count_in_threshold(gsv_values, curr_threshold)
+        num_genes_in_threshold = num_genes_in_threshold if curr_threshold[0] == 'None' else gene_counts[float(curr_threshold[0])]
+    elif threshold_type == 4 or threshold_type == 5:
+        if len(curr_threshold) == 1:
+            curr_threshold.append('0')
+        num_genes_in_threshold = calc_genes_in_threshold_range(gsv_values, curr_threshold[0], curr_threshold[1])
+
     show_gene_list = True
     # get value for the alt-gene-id column
     # if this is a 'stub' geneset.gene_id_type might not be valid,
@@ -2876,6 +2914,7 @@ def render_viewgeneset_main(gs_id, curation_view=None, curation_team=None, curat
         totalGenes=numgenes,
         uploaded_as=uploaded_as,
         threshold_value=threshold_value,
+        num_genes_in_threshold = num_genes_in_threshold,
         #SRP IMPLEMENTATION
         srp=srp
         #SRP IMPLEMENTATION END

src/templates/genesetMeta.html

@@ -43,6 +43,15 @@
                         <p>{{ threshold_value }}</p>
                     </div>
                 </div>
+
+                <div class="row">
+                    <div class="col-md-2">
+                        <p class="text-right"><strong>GENES IN THRESHOLD:</strong></p>
+                    </div>
+                    <div class="col-md-10">
+                        <p>{{ num_genes_in_threshold }}</p>
+                    </div>
+                </div>
             {% endif %}
 
             <div class="row">

src/templates/viewThreshold_new.html

@@ -42,6 +42,7 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
                                 {% else %}
                                     {{ threshold[1] }}
                                 {% endif %}
+                                ( genes count: {{ curr_gene_count }} )
                             </p>
                         </div>
                     {% else %}
@@ -95,6 +96,9 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
                     <div class="row">
                         <div id="myHisPlot" style="width:100%; height:500px;"></div>
                     </div>
+                     <div class="row">
+                        <p>* Selected threshold range in red color</p>
+                     </div>
                     <div class="row">
                         <p id="selectedGeneCount"></p>
                     </div>
@@ -237,9 +241,9 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
                       Plotly.restyle(plotElement, {
                         selectedpoints: [indices],
                         selected: {
-                         marker: {
-                            color: '#ff0000'
-                         }
+                             marker: {
+                                color: '#ff0000'
+                             }
                         }
                       });
                       //update gene count display
@@ -260,12 +264,8 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
                     var x_bin_size = 0.5;
                     if (v_max - v_min < 100) { x_bin_size = 0.1 };
                     if (v_max - v_min < 1) { x_bin_size = 0.01 };
-                    var x_bin_conf = {};
-                    if (threshold_type === 4 || threshold_type === 5) {
-                        x_bin_conf = {size: x_bin_size}
-                    } else {
-                        x_bin_conf = {start:0, size: x_bin_size}
-                    }
+                    var x_bin_conf = {size: x_bin_size};
+
 
                     //buttons to remove from plotly bar
                     var btns2rm = [ 'toggleSpikelines',  'lasso2d', 'hoverClosestCartesian', 'hoverCompareCartesian']
@@ -292,7 +292,8 @@ <h2 class="panel-title"><strong>Set GeneSet Threshold</strong></h2>
                           xaxis: {
                               title: {
                                   text: "Threshold Range"
-                              }
+                              },
+                              range: [v_min, v_max]
                           },
                           yaxis: {
                               title: {

src/templates/viewgenesetdetails.html

@@ -115,6 +115,7 @@ <h3 class="panel-title">Gene List &bull; {{ totalGenes }} Genes</h3>
             <div class="row">
                 <div class="col-xs-12 col-md-9">
                     <div class="row">
+                        <p>Genes in threshold: {{ num_genes_in_threshold }}</p>
                     </div>
                 </div>
                 <div class="col-xs-6 col-md-3" style="margin:0; padding:0;">