Limits and labels for plots.

Author: scastlara

Diff for: NetExplorer/models.py

@@ -1750,6 +1750,8 @@ class ScatterPlot(object):
     '''
     def __init__(self):
         self.traces = dict()
+        self.limits = { 'x': list(), 'y': list()}
+        self.units = dict()
 
     def add_trace(self, name):
         if name not in self.traces:
@@ -1770,6 +1772,12 @@ def add_name(self, trace_name, name):
         if trace_name in self.traces:
             self.traces[trace_name].names.append(name)
 
+    def set_limits(self, axis, start, end):
+        if axis == 'x' or axis == 'y':
+            self.limits[axis] =[start, end]
+        else:
+            raise ValueError("Axis should be 'x' or 'y'.")
+
     def plot(self):
         theplot = dict()
         theplot['data'] = list()
@@ -1790,6 +1798,16 @@ def plot(self):
             if trace.names:
                 trace_data['text'] = trace.names
             theplot['data'].append(trace_data)
+        theplot['layout'] = {'xaxis': dict(), 'yaxis': dict()}
+        if self.limits:
+            if 'x' in self.limits:
+                theplot['layout']['xaxis']['range'] = self.limits['x']
+            if 'y' in self.limits:
+                theplot['layout']['yaxis']['range'] = self.limits['y']
+        if self.units:
+            for axis, units in self.units.items():
+                axis_name = axis + 'axis'
+                theplot['layout'][axis_name]['title'] = units
         return theplot
 
     def add_color_to_trace(self, trace_name, colors):
@@ -1798,6 +1816,21 @@ def add_color_to_trace(self, trace_name, colors):
         else:
             raise(KeyError("Trace %s not found in ScatterPlot!" % trace_name))
 
+    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'.")
 
 
 class PlotlyTrace(object):
@@ -1947,7 +1980,7 @@ def get_allowed_datasets(cls, user):
             all_allowed = public_datasets | restricted_allowed
             return all_allowed
 
-    def __unicode__(self):
+    def __str__(self):
        return self.name
 
 
@@ -1956,7 +1989,7 @@ class UserDatasetPermission(models.Model):
     user = models.ForeignKey(User, on_delete=models.CASCADE)
     dataset = models.ForeignKey(Dataset, on_delete=models.CASCADE)
 
-    def __unicode__(self):
+    def __str__(self):
        return self.user.username + " [access to] " + self.dataset.name
 
 
@@ -1965,7 +1998,7 @@ class ExperimentType(models.Model):
     exp_type = models.CharField(max_length=50)
     description = models.TextField()
 
-    def __unicode__(self):
+    def __str__(self):
        return self.exp_type
 
 
@@ -2015,15 +2048,15 @@ def to_json(self):
         json_string = json.dumps(json_dict)
         return json_string
 
-    def __unicode__(self):
+    def __str__(self):
        return self.name
 
 # ------------------------------------------------------------------------------
 class ExperimentDataset(models.Model):
     dataset = models.ForeignKey(Dataset, on_delete=models.CASCADE)
     experiment = models.ForeignKey(Experiment, on_delete=models.CASCADE)
 
-    def __unicode__(self):
+    def __str__(self):
        return self.experiment.name + ' - ' + self.dataset.name
 
 
@@ -2032,7 +2065,7 @@ class UserExperimentPermission(models.Model):
     user = models.ForeignKey(User, on_delete=models.CASCADE)
     experiment = models.ForeignKey(Experiment, on_delete=models.CASCADE)
 
-    def __unicode__(self):
+    def __str__(self):
        return self.user.username + " [access to] " + self.experiment.name
 
 
@@ -2046,7 +2079,7 @@ class ConditionType(models.Model):
     name = models.CharField(max_length=50)
     description = models.TextField()
 
-    def __unicode__(self):
+    def __str__(self):
        return self.name
 
 
@@ -2062,7 +2095,7 @@ class Condition(models.Model):
     cell_type = models.CharField(max_length=50)
     description = models.TextField()
 
-    def __unicode__(self):
+    def __str__(self):
        return self.name + " - " + self.experiment.name
 
 
@@ -2071,7 +2104,7 @@ class Sample(models.Model):
     experiment = models.ForeignKey(Experiment, on_delete=models.CASCADE)
     sample_name  = models.CharField(max_length=50)
 
-    def __unicode__(self):
+    def __str__(self):
        return self.sample_name + " - " + self.experiment.name
 
 
@@ -2081,7 +2114,7 @@ class SampleCondition(models.Model):
     sample = models.ForeignKey(Sample, on_delete=models.CASCADE)
     condition = models.ForeignKey(Condition, on_delete=models.CASCADE)
 
-    def __unicode__(self):
+    def __str__(self):
        return self.experiment.name + " - " + self.sample.sample_name + " - " + self.condition.name
 
 # ------------------------------------------------------------------------------
@@ -2100,7 +2133,7 @@ class ExpressionAbsolute(models.Model):
     expression_value = models.FloatField()
     units = models.CharField(max_length=10)
 
-    def __unicode__(self):
+    def __str__(self):
         name_str = self.experiment.name + " - "
         name_str += str(self.sample.sample_name) + " - "
         name_str += str(self.gene_symbol) + ": "
@@ -2128,7 +2161,7 @@ class ExpressionRelative(models.Model):
     fold_change = models.FloatField()
     pvalue = models.FloatField()
 
-    def __unicode__(self):
+    def __str__(self):
         name_str = self.experiment.name + " - "
         name_str += self.condition1.name + " vs "
         name_str += self.condition2.name + " - "

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

@@ -2022,6 +2022,13 @@ kbd {
     background-color: #f4f4f4; 
 }
 
+#volcano-plot {
+    display: inline-block; 
+    height: 500px; 
+    min-width: 700px; 
+    background-color: #f4f4f4; 
+}
+
 #plot-genenotfound { 
     display: none; 
     margin: auto;

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

@@ -144,16 +144,14 @@ var PlanExp = (function() {
     }
 
     /**
-     * experimentDGETable
+     * getDatasets
      *   Summary:
-     *     Performs AJAX query to /experiment_dge_table, 
-     *     retrieving the HTML code of the differential
-     *     expression table and puting it in targetDiv.
+     *     
+     *     
      *   Arguments:
-     *     - Experiment name string
-     *     - jQuery object of div to put the table.
+     *    
      *   Returns:
-     *     - Nothing
+     *    
      */
     getDatasets = function(expName, datasetSelect) {
         datasetRow = function(datasetName) {
@@ -214,9 +212,10 @@ var PlanExp = (function() {
                     $("#dge-table-notfound").show(250);
                 } else {
                     $("#dge-table-notfound").hide();
-                    targetDiv.html(data);
+                    targetDiv.html(data.table);
                     targetDiv.hide();
                     targetDiv.show(250);
+                    Plotly.newPlot("volcano-plot", data.volcano);
                 }
             }
         });
@@ -341,6 +340,8 @@ var PlanExp = (function() {
         $('#planexp-dge-c1').selectpicker('val', '');
         $('#planexp-dge-c2').selectpicker('val', '');
         $("#expression-plot").html("");
+        $("#plot-tsne").html("");
+        $("#volcano-plot").html("");
         $("#plot-genenotfound").hide();
 
         // Change DGE table ConditionType select
@@ -377,7 +378,9 @@ var PlanExp = (function() {
         if ( ! condition1 || ! condition2 ) {
             return;
         } 
-
+        
+        // Clean volcano plot 
+        $("#volcano-plot").html("");
         experimentDGETable(expName, dataset, condition1, condition2, $("#planexp-dge-table"));
 
     });

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

@@ -101,6 +101,11 @@ <h4>Select conditions to compare</h4>
                 </div>
                 <div id="planexp-dge-table">
                 </div>
+
+                <div id="plot-container">
+                    <div id="volcano-plot">
+                    </div>
+                </div>
             </div> <!-- Differential expression table -->
 
             <!-- Gene Expression Plot-->

Diff for: NetExplorer/views/common.py

@@ -4,6 +4,7 @@
 from django.http        import HttpResponse
 from django.template    import RequestContext
 from NetExplorer.models import *
+from django.db.models import Func, F
 from subprocess import Popen, PIPE, STDOUT
 from django.contrib.staticfiles.templatetags.staticfiles import static
 from django.contrib.auth.models import User

Diff for: NetExplorer/views/experiment_dge_table.py

@@ -1,9 +1,49 @@
 from .common import *
 
+
+def do_volcano_plot(expression):
+    '''
+    Creates a Volcano plot with a given comparison of conditions.
+    '''
+    theplot = ScatterPlot()
+    trace_name = "Volcano Plot"
+    theplot.add_trace(trace_name)
+    max_x = 0
+    min_x = 0
+    max_y = 0
+    for gexp in expression:
+        x = gexp.fold_change
+        y = -(math.log10(gexp.pvalue))
+        theplot.add_x(trace_name, x)
+        theplot.add_y(trace_name, y)
+        theplot.add_name(trace_name, gexp.gene_symbol)
+
+        # Get max and min X
+        if min_x == 0:
+            min_x = x
+        if x > max_x:
+            max_x = x
+        elif x < min_x:
+            min_x = x
+
+        # Get max and min Y
+        if y > max_y:
+            max_y = y
+
+    bigger_x = max([abs(min_x), abs(max_x)]) + 1
+    theplot.set_limits('x', -bigger_x, bigger_x)
+    theplot.set_limits('y', 0, max_y + max_y * 0.10) # Add +10% to make plot axis more visible
+    theplot.add_units('x', 'log10 ( Fold Change ) ')
+    theplot.add_units('y', '-log10 ( pvalue ) ')
+    return theplot
+
+
 def experiment_dge_table(request):
     """
     View from PlanExp that returns the HTML of a table comparing two conditions
     """
+    max_genes = 250
+    pvalue_threshold = 0.001
     if request.is_ajax():
         exp_name = request.GET['experiment']
         c1_name = request.GET['condition1']
@@ -15,17 +55,23 @@ def experiment_dge_table(request):
         condition2 = Condition.objects.get(name=c2_name, experiment=experiment)
         expression = ExpressionRelative.objects.filter(
             experiment=experiment, dataset=dataset, 
-            condition1=condition1, condition2=condition2).order_by('-fold_change')[:500]
+            condition1=condition1, condition2=condition2, pvalue__lte=pvalue_threshold)
         if not expression:
             # In case condition1 and condition2 are reversed in Database
             expression = ExpressionRelative.objects.filter(
                 experiment=experiment, dataset=dataset, 
-                condition1=condition2, condition2=condition1).order_by('-fold_change')[:500]
-        if not expression:
-            response = {}
-            return HttpResponse(json.dumps(response), content_type="application/json")
-        else:
-            response = { 'expressions' : expression, 'database': dataset }
-            return render(request, 'NetExplorer/experiment_dge_table.html', response)
+                condition1=condition2, condition2=condition1, pvalue__lte=pvalue_threshold)
+
+        expression = expression.annotate(abs_fold_change=Func(F('fold_change'), function='ABS')).order_by('-abs_fold_change')[:max_genes]
+        response = dict()
+        if expression:
+            response_to_render = { 'expressions' : expression, 'database': dataset }
+            response['table'] = render_to_string('NetExplorer/experiment_dge_table.html', response_to_render)
+            response['volcano'] = do_volcano_plot(expression).plot()
+            try:
+                json.dumps(response)
+            except Exception as err:
+                print(err)
+        return HttpResponse(json.dumps(response), content_type="application/json")
     else:
         return render(request, 'NetExplorer/404.html')