Added LinePlot used by Affy importer.

system/plots.py

@@ -9,6 +9,7 @@ from matplotlib.axes import Subplot
 from matplotlib.figure import Figure
 from matplotlib.numerix import arange, sin, pi
 from matplotlib.widgets import RectangleSelector
+from matplotlib import cm
 from system import logger
 
 
@@ -59,6 +60,7 @@ class Plot (gtk.Frame):
         self.sel_obj = None
         self.active = False
         self.title = title
+        self.project = None
 
     def get_title(self):
         return self.title
@@ -344,6 +346,58 @@ class SinePlot(Plot):
         return self._toolbar
 
 
+class LinePlot(Plot):
+    def __init__(self, dataset, name="Line plot"):
+        Plot.__init__(self, name)
+        fig = Figure(figsize=(5,4), dpi=72)
+        self.canvas = FigureCanvas(fig)
+
+        self.ax = ax = fig.add_subplot(111)
+        self._dataset = dataset
+
+        import rpy
+        silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
+
+        rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", dataset.get_matrix())        
+        ymin, ymax = rpy.r("range(m)*1.1")
+        self._ymin, self._ymax = ymin, ymax
+        silent_eval("res <- apply(m, 2, density, from=%s, to=%s)" % (ymin, ymax))
+        silent_eval("k <- sapply(1:length(res), function(id) rev(res[[id]]$y))")
+        self._bg_matrix = bg_matrix = rpy.r("k")
+        rpy.r.rm(["k", "res", "m"])
+        
+        self.update(None)
+
+        self.add(self.canvas)
+        self.canvas.show()
+
+        # We use a regular toolbar as we don't need selections
+        self._toolbar = NavigationToolbar2(self.canvas, None)
+        self._toolbar.set_property('show-arrow', False)
+
+    def get_toolbar(self):
+        self.canvas.draw()
+        return self._toolbar
+
+    def update(self, key):
+        self.ax.clear()
+        
+        rows, cols = self._bg_matrix.shape
+        self.ax.imshow(self._bg_matrix, cmap=cm.gray, extent=(0.5, cols+0.5, self._ymin, self._ymax))
+
+        if self.project:
+            curr_sel = self.project.get_selection() # get selection object
+            ids = curr_sel['ids'] # current identifiers
+            index = [ind for id,ind in self._dataset['ids'].items() if id in ids] #conversion to index
+            for i in index:
+                line = self._dataset.get_matrix()[i]
+                self.ax.plot(range(1, len(line)+1), line)
+            
+        self.ax.set_xlim((0.5, cols+0.5))
+        self.ax.set_ylim((self._ymin, self._ymax))
+        self.canvas.draw()
+
+
 class ScatterPlot(Plot):
     def __init__(self, dataset,id_dim, sel_dim,id_1,id_2):
         Plot.__init__(self, 'Scatter plot')

workflows/go_workflow.py

@@ -216,7 +216,9 @@ class CelFileImportFunction(workflow.Function):
                 rpy.r.rm(["E", "m"])
                 
                 if m:
-                    return [dataset.Dataset(m, (('ids', rownames), ('filename', colnames)), name="AffyMatrix Data")] 
+                    data = dataset.Dataset(m, (('ids', rownames), ('filename', colnames)), name="AffyMatrix Data")
+                    plot = plots.LinePlot(data, "Gene profiles")
+                    return [data, plot]
                 else:
                     logger.log("notice", "No data loaded from importer.")
         finally:
@@ -250,6 +252,6 @@ class PCAFunction(workflow.Function):
 
         loading_plot1 = plots.ScatterPlot(P,'ids','component','1','2')
         loading_plot2 = plots.ScatterPlot(P,'ids','component','3','4')
-        score_plot = plots.ScatterPlot(T,'filename','component','1','2')     
+        score_plot = plots.ScatterPlot(T,'filename','component','1','2')
         
         return [T, P, loading_plot1, loading_plot2, score_plot]