DistanceToSelectionFunction

workflows/gobrowser.py

@@ -297,6 +297,42 @@ class GOWeightDialog(gtk.Dialog):
         options['rank_threshold'] = self._rank_spin.get_value()
         
 
+class DistanceToSelectionFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'dist-to-sel', 'Dist. to Selection')
+        self.options = DistanceToSelectionOptions()
+
+    def run(self, similarities, selection):
+        self.show_gui(similarities, self.options)
+
+        retval = []
+
+        dims = similarities.get_dim_name()
+        if dims[0] != "_%s" %dims[1] and dims[1] != "_%s" %dims[0]:
+            logger.log('warning', 'Are you sure this is a similarity matrix?')
+
+        dim = dims[0]
+        print "dim", dim
+       
+        print "selection", selection[dim]
+        print "indices", similarities.get_indices(dim, selection[dim])
+        indices = similarities.get_indices(dim, selection[dim])
+        m = apply_along_axis(max, 1, similarities.asarray().take(indices, 1))
+        retval.append(dataset.Dataset(m, [(dim, similarities[dim]),
+                                          ("_dummy", '0')]))
+        
+        return retval
+
+    def show_gui(self, similarities, options, edit=True):
+        dialog = DistanceToSelectionOptionsDialog([similarities], self.options)
+        response = dialog.run()
+        dialog.hide()
+        if response == gtk.RESPONSE_OK:
+            dialog.set_output()
+            return dialog.get_options()
+        else:
+            return options
+
 class GOWeightFunction(workflow.Function):
     def __init__(self):
         workflow.Function.__init__(self, 'load-go-ann', 'GO Influence')
@@ -334,6 +370,11 @@ class GOWeightFunction(workflow.Function):
             return options
 
 
+class DistanceToSelectionOptionsDialog(workflow.OptionsDialog):
+    def __init__(self, data, options):
+        workflow.OptionsDialog.__init__(self, data, options, ['X'])
+
+                                        
 class TTestOptionsDialog(workflow.OptionsDialog):
 
     def __init__(self, data, options):
@@ -373,13 +414,13 @@ class TTestFunction(workflow.Function):
 
         print "Out data:", self.options['out_data']
         tds = dataset.Dataset(tscores[0], [('gene_id', x['gene_id']), 
-                                           ('t', ['0'])],
+                                           ('_t', ['0'])],
                               name='t-values')
         if 't-value' in self.options['out_data']:
             retval.append(tds)
             
         pds = dataset.Dataset(tscores[1], [('gene_id', x['gene_id']), 
-                                           ('p', ['0'])],
+                                           ('_p', ['0'])],
                               name='p-values')
         if 'p-value' in self.options['out_data']:
             retval.append(pds)
@@ -387,6 +428,14 @@ class TTestFunction(workflow.Function):
         if ProbabilityHistogramPlot in self.options['out_plots']:
             retval.append(ProbabilityHistogramPlot(pds))
 
+        if VolcanoPlot in self.options['out_plots']:
+            fc = apply_along_axis(mean, 0, ns) / apply_along_axis(mean, 0, cs)
+            fcds = dataset.Dataset(fc, [('gene_id', x['gene_id']),
+                                        ('_dummy', ['0'])],
+                                   name="Fold change")
+
+            retval.append(VolcanoPlot(fcds, pds, 'gene_id'))
+
         return retval
 
     def show_gui(self, x, categories):
@@ -404,13 +453,20 @@ class TTestOptions(workflow.Options):
 
     def __init__(self):
         workflow.Options.__init__(self)
-        self['all_plots'] = [(ProbabilityHistogramPlot, 'Histogram', True)]
+        self['all_plots'] = [(ProbabilityHistogramPlot, 'Histogram', True),
+                             (VolcanoPlot, 'Histogram', True)]
         self['all_data'] = [('t-value', 't-values', True),
                             ('p-value', 'Probabilities', True),
                             ('categories', 'Categories', False)]
         self['out_data'] = ['t-value', 'p-value']
 
 
+class DistanceToSelectionOptions(workflow.Options):
+    def __init__(self):
+        workflow.Options.__init__(self)
+        self['all_data'] = [('mindist', 'Minimum distance', True)]
+
+        
 class GOWeightOptions(workflow.Options):
     def __init__(self):
         workflow.Options.__init__(self)
@@ -420,6 +476,13 @@ class GOWeightOptions(workflow.Options):
 
 class ProbabilityHistogramPlot(plots.HistogramPlot):
     def __init__(self, ds):
-        plots.HistogramPlot.__init__(self, ds, name="Confidence")
+        plots.HistogramPlot.__init__(self, ds, name="Confidence", bins=50)
 
 
+class VolcanoPlot(plots.ScatterPlot):
+    def __init__(self, fold_ds, p_ds, dim, **kw):
+        plots.ScatterPlot.__init__(self, fold_ds, p_ds, 'gene_id', '_dummy', 
+                                   '0', '0',
+                                   name="Volcano plot", 
+                                   sel_dim_2='_p', **kw)
+