t-SNE plot added.

Author: scastlara

NetExplorer/models.py

@@ -1544,9 +1544,9 @@ class Document(models.Model):
 
 
 # ------------------------------------------------------------------------------
-class PlotlyPlot(object):
+class GenExpPlot(object):
     """
-    Class for Plotly barplots.
+    Class for Plotly barplots and violins.
     traces = [
         0 : {
             group1: [ values ],
@@ -1559,14 +1559,17 @@ class PlotlyPlot(object):
     """
     def __init__(self):
         self.traces = list()
+        self.traces_set = set()
         self.groups = list()
+        self.groups_set = set()
         self.title  = str()
         self.ylab   = str()
         self.trace_names = list()
 
     def add_group(self, group):
-        if group not in self.groups:
+        if group not in self.groups_set:
             self.groups.append(group)
+            self.groups_set.add(group)
 
         for trace in self.traces:
             if group not in trace:
@@ -1610,7 +1613,7 @@ def is_empty(self):
 
 
 # ------------------------------------------------------------------------------
-class BarPlot(PlotlyPlot):
+class BarPlot(GenExpPlot):
     """
     Class for Plotly bar plots.
     Each bar (group) consists of only one value.
@@ -1648,7 +1651,7 @@ def plot(self):
 
 
 # ------------------------------------------------------------------------------
-class ViolinPlot(PlotlyPlot):
+class ViolinPlot(GenExpPlot):
     """
     Class for Plotly violinplots.
     Each violin (group) is made of multiple values.
@@ -1711,6 +1714,79 @@ def plot(self):
         return theplot
 
 
+class ScatterPlot(object):
+    '''
+    Class for Plotly scatterplots
+    '''
+    def __init__(self):
+        self.traces = dict()
+    
+    def add_trace(self, name):
+        if name not in self.traces:
+            self.traces[name] = PlotlyTrace(name)
+            self.traces[name].order = len(self.traces)
+    
+    def add_x(self, trace_name, x):
+        if trace_name in self.traces:
+            self.traces[trace_name].x.append(x)
+        else:
+            raise(KeyError("Trace %s not found in ScatterPlot!" % trace_name))
+
+    def add_y(self, trace_name, y):
+        if trace_name in self.traces:
+            self.traces[trace_name].y.append(y)
+    
+    def add_name(self, trace_name, name):
+        if trace_name in self.traces:
+            self.traces[trace_name].names.append(name)
+
+    def plot(self):
+        theplot = dict()
+        theplot['data'] = list()
+        theplot['layout'] = dict()
+        for trace_name in sorted(self.traces.keys(), key=lambda n: self.traces[n].order):
+            trace = self.traces[trace_name]
+            trace_data = dict()
+            if str(trace_name).isdigit():
+                trace_data['name'] = 'c' + str(trace.name)
+            else:
+                trace_data['name'] = str(trace.name)
+            trace_data['x'] = trace.x
+            trace_data['y'] = trace.y
+            trace_data['type'] = trace.type
+            trace_data['mode'] = trace.mode
+            if trace.color:
+                trace_data['marker'] = { 'color': list(trace.color) }
+            if trace.names:
+                trace_data['text'] = trace.names
+            theplot['data'].append(trace_data)
+        return theplot
+    
+    def add_color_to_trace(self, trace_name, colors):
+        if trace_name in self.traces:
+            self.traces[trace_name].color = colors
+        else:
+            raise(KeyError("Trace %s not found in ScatterPlot!" % trace_name))
+
+
+
+class PlotlyTrace(object):
+    '''
+    Class for plotly traces
+    '''
+    def __init__(self, name):
+        self.name = name
+        self.order = int()
+        self.x = list()
+        self.y = list()
+        self.names = list()
+        self.mode = 'markers'
+        self.type = 'scatter'
+        self.color = list()
+
+    
+
+
 
 
 # EXCEPTIONS
@@ -2002,6 +2078,13 @@ def __unicode__(self):
         name_str += self.units
         return name_str
 
+    
+class CellPlotPosition(models.Model):
+    experiment = models.ForeignKey(Experiment, on_delete=models.CASCADE)
+    sample = models.ForeignKey(Sample, on_delete=models.CASCADE)
+    dataset = models.ForeignKey(Dataset, on_delete=models.CASCADE)
+    x_position = models.FloatField()
+    y_position = models.FloatField()
 
 
 # ------------------------------------------------------------------------------

NetExplorer/static/css/style.css

@@ -2004,7 +2004,7 @@ kbd {
 #select-dataset { display: none; }
 #planexp-gene-expression { display: none; }
 .gene-expression-search-container { width: 50%; }
-#expression-plot-container { 
+#plot-container { 
     width: 100%; 
     margin-top: 50px;
     text-align: center; 
@@ -2016,6 +2016,13 @@ kbd {
     background-color: #f4f4f4; 
 }
 
+#tsne-plot {
+    display: inline-block; 
+    height: 500px; 
+    min-width: 700px; 
+    background-color: #f4f4f4; 
+}
+
 #plot-genenotfound { 
     display: none; 
     margin: auto;
@@ -2025,6 +2032,15 @@ kbd {
     background-color: #FDD4D4;
 }
 
+#tsneplot-genenotfound {
+    display: none; 
+    margin: auto;
+    font-size: 18px;
+    padding: 8px;
+    width: 700px; 
+    background-color: #FDD4D4;  
+}
+
 #expression-plot-loading {
     display: none;
     position: absolute;
@@ -2033,10 +2049,27 @@ kbd {
     margin-top: 175px;
 }
 
+#tsne-plot-loading {
+    display: none;
+    position: absolute;
+    z-index: 2;
+    left: calc(50% - 75px);
+    margin-top: 175px;
+}
+
 .planexp-loading-img {
     width: 150px;
 }
 
 .input-grp-withlabel {
     vertical-align: bottom !important;
-}
+}
+
+#planexp-tsne { display: none; }
+
+
+#planexp-tsne input[type=range]::-moz-range-track { 
+    background: #E7E7E7;
+}
+
+#plot-tsne-btn    { width: 125px; }