Added spin buttons for minimum and maximum information content in DAG plot.

workflows/gobrowser.py

@@ -1,6 +1,6 @@
 
 import gtk
-from fluents import dataset, logger, plots, workflow, fluents, project, view
+from fluents import dataset, logger, plots, workflow, fluents, project, view, main
 import geneontology
 from matplotlib.nxutils import points_inside_poly
 import matplotlib
@@ -471,6 +471,17 @@ class TTestFunction(workflow.Function):
             return options
 
 
+class SetICFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'set-ic', 'Set IC')
+
+    def run(self, ds):
+        if 'go-terms' in ds.get_dim_name():
+            main.workflow.current_ic = ds
+        else:
+            logger.log('warning', 'Cannot use this dataset as IC on the go-terms dimension')
+        return
+        
 class PlotDagFunction(workflow.Function):
     def __init__(self):
         workflow.Function.__init__(self, 'go-dag', 'Build DAG')
@@ -553,13 +564,14 @@ class DagPlot(plots.Plot):
                  with_labels=False, name='DAG Plot'):
 
         plots.Plot.__init__(self, name)
-        self._add_ic_spin_button()
+        self._add_ic_spin_buttons()
         self.nodes = graph.nodes()
         self.graph = graph
         self._pos = pos
         self._nodesize = nodesize
         self._nodecolor = nodecolor
         self._with_labels = with_labels
+        self.visible = set()
         
         self.current_dim = dim
 
@@ -618,19 +630,33 @@ class DagPlot(plots.Plot):
         self.axes.set_frame_on(False)
         self.fig.subplots_adjust(left=0, right=1, bottom=0, top=1)
 
-    def _add_ic_spin_button(self):
+    def _add_ic_spin_buttons(self):
-        sb = gtk.SpinButton()
+        """Adds spin buttons to the toolbar for selecting minimum and maximum
-        sb.set_range(0, 100)
+        threshold values on information content."""
-        sb.set_value(1)
+        sb_min = gtk.SpinButton()
-        sb.set_increments(1, 3)
+        sb_min.set_range(0, 100)
-        label = gtk.Label("IC > ")
+        sb_min.set_value(1)
+        sb_min.set_increments(1, 3)
+        sb_min.connect('value-changed', self._on_ic_value_changed)
+        self._ic_sb_min = sb_min
+
+        sb_max = gtk.SpinButton()
+        sb_max.set_range(0, 100)
+        sb_max.set_value(1)
+        sb_max.set_increments(1, 3)
+        sb_max.connect('value-changed', self._on_ic_value_changed)
+        self._ic_sb_max = sb_max
+
+        label = gtk.Label(" < IC < ")
         hbox = gtk.HBox()
+        hbox.pack_start(sb_min)
         hbox.pack_start(label)
-        hbox.pack_start(sb)
+        hbox.pack_start(sb_max)
         ti = gtk.ToolItem()
         ti.set_expand(False)
         ti.add(hbox)
-        sb.show()
+        sb_min.show()
+        sb_max.show()
         label.show()
         hbox.show()
         ti.show()
@@ -638,7 +664,7 @@ class DagPlot(plots.Plot):
         ti.set_tooltip(self._toolbar.tooltips, "Set information content threshold")
         
     def _calc_pos(self, graph):
-        """Calculates position for graph nodes."""
+        """Calculates position for graph nodes using 'dot' layout."""
         gv_graph = networkx.DiGraph()
         for start, end in graph.edges():
             gv_graph.add_edge(start.replace('GO:', ''), end.replace('GO:', ''))
@@ -652,6 +678,43 @@ class DagPlot(plots.Plot):
                 pos[k] = v
         return pos
 
+    def set_ic_threshold(self, ic_min, ic_max):
+        """Sets Information Content min and max to the given values.
+        Updates the plot accordingly to show only values that have an
+        information content within the boundaries. Other values are
+        also excluded from being selected from the plot.
+        @param ic_min Do not show nodes with IC below this value.
+        @param ic_max Do not show nodes with IC above this value.
+        """
+        ic = getattr(main.workflow, 'current_ic', None)
+        if ic == None:
+            print "no ic set"
+            return
+        
+        icnodes = ic.existing_identifiers('go-terms', self.nodes)
+        icindices = ic.get_indices('go-terms', icnodes)
+        a = ravel(ic.asarray()[icindices])
+        ic_good = set(array(icnodes)[(a>ic_min) & (a<ic_max)])
+
+        sizes = zeros(len(self.nodes))
+        visible = set()
+        for i, n in enumerate(self.nodes):
+            if n in ic_good:
+                sizes[i] = 50
+                visible.add(n)
+            else:
+                sizes[i] = 0
+        self.visible = visible
+        
+        self.node_collection._sizes = sizes
+        self.canvas.draw()
+        
+    def _on_ic_value_changed(self, sb):
+        """Callback on spin button value changes."""
+        ic_min = self._ic_sb_min.get_value()
+        ic_max = self._ic_sb_max.get_value()
+        self.set_ic_threshold(ic_min, ic_max)
+    
     def rectangle_select_callback(self, x1, y1, x2, y2, key):
         ydata = self.yaxis_data
         xdata = self.xaxis_data
@@ -665,7 +728,7 @@ class DagPlot(plots.Plot):
         assert y1<=y2
         
         index = nonzero((xdata>x1) & (xdata<x2) & (ydata>y1) & (ydata<y2))[0]
-        ids = [self.nodes[i] for i in index]
+        ids = self.visible.intersection([self.nodes[i] for i in index])
         ids = self.update_selection(ids, key)
         self.selection_listener(self.current_dim, ids)
 

workflows/smokers.py

@@ -54,6 +54,7 @@ class SmallTestWorkflow(workflow.Workflow):
         # Gene Ontology
         go = workflow.Stage('go', 'Gene Ontology')
         go.add_function(gobrowser.LoadGOFunction())
+        go.add_function(gobrowser.SetICFunction())
         # go.add_function(gobrowser.GOWeightFunction())
         # go.add_function(gobrowser.DistanceToSelectionFunction())
         # go.add_function(gobrowser.TTestFunction())