category data and plot selection update|

system/annotations.py

@@ -1,6 +1,9 @@
 
 from sets import Set as set
 set.update = set.union_update
+import dataset
+import scipy
+
 
 class AnnotationsException(Exception):
     pass
@@ -63,3 +66,28 @@ class Annotations:
         """
         return self.dimensions.has_key(dim)
 
+    def to_dataset(self,dim):
+        """ Returns a dataset representation of annotations.
+        """
+        if self.has_dimension(dim):
+            num_dim1 = len(set(self.dimensions[dim])) #number of unique genes
+            all_genes = set(self.dimensions[dim])
+            all_categories = set()
+            for cat in self.dimensions[dim].values():
+                all_categories.update(cat)
+            num_dim1 = len(all_genes) #number of unique genes
+            num_dim2 = len(all_categories) #number of unique categories
+            gene_list=[]
+            cat_list=[]
+        matrix = scipy.zeros((num_dim1,num_dim2),'bwu')
+        for i,gene in enumerate(all_genes):
+            gene_list.append(gene)
+            for j,cat in enumerate(all_categories):
+                cat_list.append(cat)
+                matrix[i,j] = 1
+        def_list = [['genes',gene_list],['go',cat_list]]
+
+        return dataset.Dataset(matrix,def_list)
+        
+        
+