Checking if gene exist for tsne-plot

Author: scastlara

Diff for: NetExplorer/models.py

@@ -1565,6 +1565,7 @@ def __init__(self):
         self.title  = str()
         self.ylab   = str()
         self.trace_names = list()
+        self.units = dict()
 
     def add_group(self, group):
         if group not in self.groups_set:
@@ -1609,7 +1610,24 @@ def is_empty(self):
                     empty = False
                     break
         return empty
-                
+    
+    def add_units(self, axis, units):
+        '''
+        Adds units to one axis of the plot.
+
+        Args:
+            axis: string cointaining 'x' or 'y'.
+            units: string for units.
+        
+        Returns:
+            nothing
+        '''
+        if axis == 'x' or axis == 'y':
+            self.units[axis] = units
+        else:
+            raise ValueError("Axis should be a string containing 'x' or 'y'.")
+            
+
 
 
 # ------------------------------------------------------------------------------
@@ -1647,8 +1665,15 @@ def plot(self):
         if self.ylab:
             theplot['layout']['yaxis'] = dict()
             theplot['layout']['yaxis']['title'] = self.ylab
+        
+        if self.units:
+            for axis, units in self.units.items():
+                axis_name = axis + 'axis'
+                theplot['layout'][axis_name] = dict()
+                theplot['layout'][axis_name]['title'] = units
         return theplot
-
+    
+    
 
 # ------------------------------------------------------------------------------
 class ViolinPlot(GenExpPlot):
@@ -1711,6 +1736,11 @@ def plot(self):
         if self.ylab:
             theplot['layout']['yaxis'] = dict()
             theplot['layout']['yaxis']['title'] = self.ylab
+        if self.units:
+            for axis, units in self.units.items():
+                axis_name = axis + 'axis'
+                theplot['layout'][axis_name] = dict()
+                theplot['layout'][axis_name]['title'] = units
         return theplot
 
 

Diff for: NetExplorer/static/css/style.css

@@ -2031,7 +2031,7 @@ kbd {
     background-color: #FDD4D4;
 }
 
-#tsneplot-genenotfound {
+#tsne-plot-genenotfound {
     display: none; 
     margin: auto;
     font-size: 18px;

Diff for: NetExplorer/static/js/planexp.js

@@ -281,7 +281,7 @@ var PlanExp = (function() {
                     console.log(data.data);
                     Plotly.newPlot(plotDivId, data.data, data.layout);
                 } else {
-                    $("#plot-genenotfound").show(250);
+                    $("#tsne-plot-genenotfound").show(250);
                 }
                 $("#tsne-plot-loading").hide();
             }
@@ -419,12 +419,12 @@ var PlanExp = (function() {
             withcolor = true;
             ctype = "Cluster";
             if (!geneName) {
-                $("#tsneplot-genenotfound").show(250);
+                $("#tsne-plot-genenotfound").show(250);
                 return;
             }
         }
 
-        $("#tsneplot-genenotfound").hide();
+        $("#tsne-plot-genenotfound").hide();
         plotTSNE(expName, dataset, geneName, withcolor, ctype, "tsne-plot");
     });
 

Diff for: NetExplorer/templates/NetExplorer/planexp.html

@@ -173,7 +173,7 @@ <h4>Color By:</h4>
 
                 <br>
                 <div id="plot-container">
-                    <div id="tsneplot-genenotfound">
+                    <div id="tsne-plot-genenotfound">
                         <span class="glyphicon glyphicon-warning-sign"></span>
                         Gene/Symbol not found
                     </div>

Diff for: NetExplorer/views/plot_gene_expression.py

@@ -6,6 +6,7 @@ def do_barplot(experiment, dataset, conditions, gene_symbols):
     Useful when we have One Sample per Condition per Gene (one value to plot).
     """
     theplot = None
+    units = None
     for g_idx, gene_symbol in enumerate(gene_symbols):
         if theplot is None:
             theplot = BarPlot()
@@ -20,21 +21,25 @@ def do_barplot(experiment, dataset, conditions, gene_symbols):
                 experiment=experiment, dataset=dataset, 
                 sample__in=samples,    gene_symbol=gene_symbol)
             if expression:
+                if units is None:
+                    units = expression[0].units
                 expression = expression[0].expression_value
             else:
                 expression = 0
             theplot.add_group(condition.name)
             theplot.add_value(expression, condition.name, g_idx)
+            
+    theplot.add_units("y", units)
     return theplot
 
 
-import time
 def do_violin(experiment, dataset, conditions, gene_symbols, ctype):
     '''
     THE CHECK
     dd_Smed_v6_7_0_1,dd_Smed_v6_702_0_1,dd_Smed_v6_659_0_1,dd_Smed_v6_920_0_1
     '''
     theplot = None
+    units = None
     for g_idx, gene_symbol in enumerate(gene_symbols):
         if theplot is None:
             theplot = ViolinPlot()
@@ -55,15 +60,17 @@ def do_violin(experiment, dataset, conditions, gene_symbols, ctype):
                 sample__in=samples,    gene_symbol=gene_symbol)
             theplot.add_group(condname)
 
-            start = time.time()
             if expression:
+                if units is None:
+                    units = expression[0].units
                 for exp in expression:
                     if exp.expression_value:
                         theplot.add_value(exp.expression_value, condname, g_idx)
                     else:
                         theplot.add_value(0, condname, g_idx)
             else:
                 expression = 0
+    theplot.add_units('y', units)
     return theplot
 
 

Diff for: NetExplorer/views/plot_tsne.py

@@ -30,13 +30,17 @@ def do_tsne(experiment, dataset, conditions, gene_symbol, ctype, with_color):
                 experiment=experiment, dataset=dataset,
                 sample__in=samples, gene_symbol=gene_symbol
             )
-            # We need a dictionary with {cell_id : cell_expression}
-            # so we can keep the same order as cell positions (in cell_order) 
-            thedict = dict()
-            for cellexp in cell_expression:
-                thedict[cellexp.sample.id] = cellexp.expression_value
-            cell_expression = [ thedict[cell_idx] for cell_idx in cell_order ]
-            theplot.add_color_to_trace(trace_name, cell_expression)
+            if cell_expression:
+                # We need a dictionary with {cell_id : cell_expression}
+                # so we can keep the same order as cell positions (in cell_order) 
+                thedict = dict()
+                for cellexp in cell_expression:
+                    thedict[cellexp.sample.id] = cellexp.expression_value
+                cell_expression = [ thedict[cell_idx] for cell_idx in cell_order ]
+                theplot.add_color_to_trace(trace_name, cell_expression)
+            else:
+                theplot = None
+                break
     return theplot
 
 
@@ -66,9 +70,9 @@ def plot_tsne(request):
 
         # Do the plot
         theplot = do_tsne(experiment, dataset, conditions, gene_symbol, ctype, with_color)
-        response = theplot.plot()
-        try:
-            json.dumps(response)
-        except Exception as err:
-            print(err)
+        if theplot is not None:
+            response = theplot.plot()
+        else:
+            response = None
+
         return HttpResponse(json.dumps(response), content_type="application/json")