fixes

system/dataset.py

@@ -57,8 +57,8 @@ class Dataset:
         else:
             raise ValueError, "Array input must be of ArrayType"
                         
-    def __str__(self):
+    #def __str__(self):
-        return self._name + ":\n" + "Dim names: " +  self._dims.__str__()
+    #    return self._name + ":\n" + "Dim names: " +  self._dims.__str__()
 
     def __iter__(self):
         """Returns an iterator over dimensions of dataset."""
@@ -181,7 +181,7 @@ class Dataset:
         if idents==None:
             index = array_sort(self._map[dim].values())
         else:
-            index = [self._map[dim][key] for key in idents]
+            index = [self._map[dim][key] for key in idents if self._map[dim].has_key(key)]
         return asarray(index)        
         
 class CategoryDataset(Dataset):
@@ -236,7 +236,7 @@ class GraphDataset(Dataset):
         
     def asnetworkx(self,nx_type='graph'):
         dim = self.get_dim_name()[0]
-        ids = self.get_identifiers(dim)
+        ids = self.get_identifiers(dim,sorted=True)
         adj_mat = self.asarray()
         G = self._graph_from_adj_matrix(adj_mat,labels=ids)
         self.has_graph = True
@@ -272,11 +272,6 @@ class GraphDataset(Dataset):
 
 Dataset._all_dims=set()
         
-class Selection:
-    """Handles selected identifiers along each dimension of a dataset"""
-    def __init__(self):
-        self.current_selection={}
-        
 class ReverseDict(dict):
     """
     A dictionary which can lookup values by key, and keys by value.
@@ -300,7 +295,7 @@ def to_file(filepath,dataset,name=None):
     """
     if not name:
         name = dataset._name
-    data = shelve.open(filepath,protocol=2)
+    data = shelve.open(filepath,flag='c',protocol=2)
     if data: #we have an append 
         names = data.keys()
         if name in names:
@@ -311,7 +306,7 @@ def to_file(filepath,dataset,name=None):
 
 def from_file(filepath):
     """Read dataset from file """
-    data = shelve.open(filepath)
+    data = shelve.open(filepath,flag='r')
     out_data = []
     for name in data.keys():
         sub_data = data[name]
@@ -324,3 +319,7 @@ def from_file(filepath):
             
     return out_data
     
+class Selection:
+    """Handles selected identifiers along each dimension of a dataset"""
+    def __init__(self):
+        self.current_selection={}

system/fluents.py

@@ -80,6 +80,8 @@ class FluentApp:
         self.init_gui()
 
     def change_plot(self, plot):
+        # add current selection to new plot
+        plot.selection_changed(self.project.get_selection())
         pt = self.widget_tree.get_widget('main_view')
         pt.insert_view(plot)
         

system/navigator.py

@@ -18,7 +18,6 @@ class NavigatorView (gtk.TreeView):
 
         # various properties
         self.set_headers_visible(False)
-
         # Selection Mode
         self.get_selection().set_mode(gtk.SELECTION_MULTIPLE)
         self.get_selection().set_select_function(self.is_selectable)
@@ -29,10 +28,10 @@ class NavigatorView (gtk.TreeView):
         #        self.connect('cursor_changed', self.cursor_changed_handler)
         self.connect('row_activated', self.row_activated_handler)
 
-        textrenderer = gtk.CellRendererText()
+        self.textrenderer = textrenderer = gtk.CellRendererText()
-
+        textrenderer.set_property('foreground_set',True)
         self.object_col = gtk.TreeViewColumn('Object')
-        self.object_col.pack_start(textrenderer)
+        self.object_col.pack_start(textrenderer,expand=False)
         self.object_col.set_attributes(textrenderer, cell_background=3, foreground=4, text=0)
         self.append_column(self.object_col)
 
@@ -51,7 +50,6 @@ class NavigatorView (gtk.TreeView):
         if paths:
             self.data_tree.drag_data_get(paths[0], selection)
 
-
     def add_project(self, project):
         self.project = project
         self.data_tree = project.data_tree
@@ -69,12 +67,13 @@ class NavigatorView (gtk.TreeView):
 
     # selection changed, setting current_data ojbects
     def selection_changed_handler(self, selection):
-                
         # update prev selection right away in case of multiple events
         model, paths = selection.get_selected_rows()
+        if not paths: # a plot is marked: do nothing
+            return
+
         tmp = self._previous_selection
         self._previous_selection = paths
-              
         # set timestamp on newly selected objects
         [self.data_tree.set_value(self.data_tree.get_iter(path),5,time.time()) for path in paths if path not in tmp]
 
@@ -99,7 +98,6 @@ class NavigatorView (gtk.TreeView):
 
         if not (treestore.get_value(iter,2) or treestore.get_value(iter,1)):
             return
-
         self.expand_to_path(pos)        
 
         if isinstance(obj,dataset.Dataset):

system/plots.py

@@ -238,6 +238,7 @@ class Plot (gtk.Frame):
         self.fig = Figure(figsize=(5,4), dpi=72)
         self.canvas = FigureCanvas(self.fig)
         self.fig.set_facecolor('white')
+
     def get_title(self):
         return self.title
 
@@ -394,6 +395,8 @@ class LineViewPlot(Plot):
     ps: slow (cant get linecollection and blit to work)
     """
     def __init__(self, dataset,major_axis=1,minor_axis=None, name="Line view"):
+        self.use_blit = False
+        self._last_index = []
         self._data = dataset.asarray()
         self.dataset = dataset
         Plot.__init__(self, name)
@@ -407,7 +410,10 @@ class LineViewPlot(Plot):
         x_axis = scipy.arrayrange(self._data.shape[minor_axis])
         for i in range(self._data.shape[major_axis]):
             yi = scipy.take(self._data,[i],axis=major_axis)
+            if self.use_blit:
                 l,=self.ax.plot(x_axis,yi,'k',alpha=.05,animated=True)
+            else:
+                l,=self.ax.plot(x_axis,yi,'k',alpha=.05)
             self.line_collection[i] = l
         
         self.add(self.canvas)
@@ -427,18 +433,33 @@ class LineViewPlot(Plot):
     def selection_changed(self, selection):
         ids = selection[self.current_dim] # current identifiers
         index = self.dataset.get_indices(self.current_dim, ids)
+        if self.use_blit:
             if self._background is None:
-            print "background needs copy"
+                self._last_index = None
                 self._background = self.canvas.copy_from_bbox(self.ax.bbox)
-        print self.ax.bbox.get_bounds()
+        
             self.canvas.restore_region(self._background)
         if index:
+            if self._last_index:
+                for i in self._last_index:
+                    # if not using blit: reset last selection
+                    self.ax.lines[i].set_color('k')
+                    self.ax.lines[i].set_alpha(.05)
+                    self.ax.lines[i].set_zorder(1)
             for i in index:
-                self.line_collection[i].set_visible(True)
+                self.ax.lines[i].set_color('r')
-                self.line_collection[i].set_color('r')
+                self.ax.lines[i].set_alpha(1.0)
-                self.line_collection[i].set_alpha(1.0)
+                self.ax.lines[i].set_visible(True)
-                self.ax.draw_artist(self.line_collection[i])
+                self.ax.lines[i].set_zorder(3)
+                if self.use_blit:
+                    self.ax.draw_artist(self.ax.lines[i])
+                #else:
+                #    self.ax.add_line(self.line_collection[i])
+                self._last_index = index
+            if self.use_blit:    
                 self.canvas.blit()
+            else:
+                self.canvas.draw()
             
 class ScatterMarkerPlot(Plot):
     """The ScatterMarkerPlot is faster than regular scatterplot, but
@@ -446,9 +467,14 @@ has no color and size options."""
     def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2, name="Scatter plot"):
         Plot.__init__(self, name)
         self.ax = ax = self.fig.add_subplot(111)
+        #self.ax.set_position([0.01,0.01,.99,.99])
+        self.ax.set_xticks([])
+        self.ax.set_yticks([])
+        self.ax.axhline(0,color='k',lw=1.5,zorder=0)
+        self.ax.axvline(0,color='k',lw=1.5,zorder=0)
         self.current_dim = id_dim
         self.dataset_1 = dataset_1
-        
+        self._selection_line = None
         x_index = dataset_1[sel_dim][id_1]
         y_index = dataset_2[sel_dim][id_2]
         
@@ -493,9 +519,9 @@ has no color and size options."""
         xdata_new = scipy.take(self.xaxis_data, index) #take data
         ydata_new = scipy.take(self.yaxis_data, index)
         #remove old selection
-        if len(self.ax.lines)>1:
+        if self._selection_line:
-            del self.ax.lines[-1]
+            self.ax.lines.remove(self._selection_line)
-        self.ax.plot(xdata_new,ydata_new,'ok')
+        self._selection_line, = self.ax.plot(xdata_new,ydata_new,'or')
         self._toolbar.forward() #update data lims before draw
         self.canvas.draw()
 
@@ -505,6 +531,7 @@ has no color and size options."""
     def __init__(self, dataset_1, dataset_2, id_dim, sel_dim, id_1, id_2,c='b',s=30, name="Scatter plot"):
         Plot.__init__(self, name)
         self.ax = ax = self.fig.add_subplot(111)
+        #self.ax.set_position([0.01,0.01,.99,.99])
         self.current_dim = id_dim
         self.dataset_1 = dataset_1
         
@@ -516,8 +543,8 @@ has no color and size options."""
         
         ax.scatter(self.xaxis_data,self.yaxis_data,s=s,c=c,faceted=False,edgecolor='k')
         ax.set_title(self.get_title())
-        ax.set_xlabel("%s - %s" % (sel_dim, id_1))
+        #ax.set_xlabel("%s - %s" % (sel_dim, id_1))
-        ax.set_ylabel("%s - %s" % (sel_dim, id_2))
+        #ax.set_ylabel("%s - %s" % (sel_dim, id_2))
 
         # collection
         self.coll = ax.collections[0]
@@ -553,8 +580,10 @@ has no color and size options."""
         ids = selection[self.current_dim] # current identifiers
         index = self.dataset_1.get_indices(self.current_dim, ids)
         lw = scipy.zeros(self.xaxis_data.shape,'f')
+        zo = lw.copy() + 1 #z-order
         scipy.put(lw,index,2.)
         self.coll.set_linewidth(lw)
+        self.coll.set_zorder(zo)
         self._toolbar.forward() #update data lims before draw
         self.canvas.draw()
         
@@ -598,6 +627,9 @@ class NetworkPlot(Plot):
             kw.pop('node_color')
 
         self.ax = self.fig.add_subplot(111)
+        self.ax.set_position([0.01,0.01,.99,.99])
+        self.ax.set_xticks([])
+        self.ax.set_yticks([])
         # FIXME: ax shouldn't be in kw at all
         if kw.has_key('ax'):
             kw.pop('ax')
@@ -659,7 +691,7 @@ class NetworkPlot(Plot):
         self.ax.clear()
         networkx.draw_networkx_edges(self.graph, edge_list=self.graph.edges(), \
             ax=self.ax, **self.keywords)
-        
+        networkx.draw_networkx_labels(self.graph,**self.keywords)
         if unselected_nodes:
             networkx.draw_networkx_nodes(self.graph, nodelist=unselected_nodes, \
                 node_color='r', node_size=unselected_sizes, ax=self.ax, **self.keywords)

system/project.py

@@ -2,6 +2,7 @@
 import scipy
 import gobject
 import gtk
+import logger
 from system import dataset, plots
 
 class Project:
@@ -70,11 +71,17 @@ class Project:
         it = self.data_tree_insert(parent_iter, fun, None, "grey","black")
 
         for d in data:
-            if isinstance(d, dataset.Dataset):
+            if isinstance(d, dataset.GraphDataset):
                 self.add_dataset(d)
-                self.data_tree_insert(it, d.get_name(), d, "white", "blue")
+                self.data_tree_insert(it, d.get_name(), d, "LightPink", "black")
+            elif isinstance(d,dataset.CategoryDataset):
+                self.add_dataset(d)
+                self.data_tree_insert(it, d.get_name(), d, "LightSalmon", "black")
+            elif isinstance(d, dataset.Dataset):
+                self.add_dataset(d)
+                self.data_tree_insert(it, d.get_name(), d, "LightSkyBlue", "black")
             elif isinstance(d, plots.Plot):
-                self.data_tree_insert(it, d.get_title(), d, "white", "dark green")
+                self.data_tree_insert(it, d.get_title(), d, "PaleGreen", "black")
                 d.set_selection_listener(self.set_selection)
                 self._selection_observers.append(d)
 
@@ -91,6 +98,7 @@ class Project:
 
     def add_dataset(self,dataset):
         """Appends a new Dataset to the project."""
+        logger.log('debug','Adding dataset: %s' %dataset.get_name())
         self.datasets.append(dataset)
         for dim_name in dataset.get_all_dims():
             if dim_name not in self.dim_names:

workflows/pca_workflow.py

@@ -6,6 +6,8 @@ from scipy import log2,transpose,dot,divide,shape,mean,resize,zeros
 from scipy.linalg import svd,inv,norm,get_blas_funcs,eig
 from system import dataset, logger, plots
 
+
+
 class PCAWorkflow(wf.Workflow):
     name = 'PCA Workflow'
     ident = 'pca'
@@ -96,9 +98,9 @@ class PCAFunction(Function):
         row_ids = data.get_identifiers('genes')
         col_ids = data.get_identifiers('samples')
         
-        T = dataset.Dataset(T,[('samples',col_ids) ,comp_def])
+        T = dataset.Dataset(T,[('samples',col_ids) ,comp_def],name='T2')
-        P = dataset.Dataset(P,[('genes',row_ids),comp_def])
+        P = dataset.Dataset(P,[('genes',row_ids),comp_def],name='P')
-        E = dataset.Dataset(E,[('samples',col_ids),('genes',row_ids)])
+        E = dataset.Dataset(E,[('samples',col_ids),('genes',row_ids)],name='E')
         #tsq = dataset.Dataset(tsq,[singel_def,data_ids[1])
         
         ## plots