now saves Venn figure files as PNG (and also generates projection Venn

diagrams

svn path=/; revision=573

diff --git a/Personnel/preecej/python_singletons/incomparanoid.py b/Personnel/preecej/python_singletons/incomparanoid.py
index 917fc07b4b181975557b55ce198f2b90a8b2aa2c..4cb4804d9c4a9e3c00df8fba5232a202a706c3e5 100755 (executable)
--- a/Personnel/preecej/python_singletons/incomparanoid.py
+++ b/Personnel/preecej/python_singletons/incomparanoid.py
@@ -258,7 +258,7 @@ def compare_maps(dict_cmp_map, dict_inp_map, comparison_file_path, compara_outpu
         CMP_OUT_FILE.close()
         CMP_FLAT_OUT_FILE.close()
 
-    return [set_inp_ref_loci, set_cmp_ref_loci]
+    return [[set_inp_ref_loci, set_cmp_ref_loci], [inp_exc_prj_loci, cmp_exc_prj_loci, intersection_prj_loci]]
 
 #----------------------------------------------------------------------------------------------------------------------
 def write_reactome_files(dict_map, reactome_gene_protein_path, reactome_projection_path, projection_prefix) :
@@ -282,18 +282,27 @@ def write_reactome_files(dict_map, reactome_gene_protein_path, reactome_projecti
 
 
 #----------------------------------------------------------------------------------------------------------------------
-def generate_venn(venn_data, colors, is_ref, ref_species, proj_species, reciprocal_id, confidence) :
+def generate_venn(venn_data, colors, is_ref, ref_species, proj_species, reciprocal_id, confidence, venn_output_path) :
 #----------------------------------------------------------------------------------------------------------------------
     """build and display Venn diagrams representing reference loci overlap"""
 
-    intersection_loci = len(venn_data[0] & venn_data[1])
-    union_loci = len(venn_data[0] | venn_data[1])
-    inp_exc_loci = len(venn_data[0] - venn_data[1])
-    cmp_exc_loci = len(venn_data[1] - venn_data[0])
+    plt.figure(figsize=(9, 7))
 
-    plt.figure(figsize=(8, 7))
+    if is_ref :
+        intersection_loci = len(venn_data[0] & venn_data[1])
+        union_loci = len(venn_data[0] | venn_data[1])
+        inp_exc_loci = len(venn_data[0] - venn_data[1])
+        cmp_exc_loci = len(venn_data[1] - venn_data[0])
+        
+        v = venn2(venn_data, ('Inparanoid', 'Compara'))
 
-    v = venn2(venn_data, ('Inparanoid', 'Compara'))
+    else :
+        intersection_loci = venn_data[2]
+        inp_exc_loci = venn_data[0]
+        cmp_exc_loci = venn_data[1]
+        union_loci = inp_exc_loci + intersection_loci + cmp_exc_loci
+        
+        v = venn2(subsets = venn_data)
     
     v.get_patch_by_id('10').set_alpha(0.5)
     v.get_patch_by_id('10').set_color(colors[0])
@@ -304,9 +313,16 @@ def generate_venn(venn_data, colors, is_ref, ref_species, proj_species, reciproc
     v.get_patch_by_id('11').set_alpha(0.75)
     v.get_patch_by_id('11').set_color(colors[2])
     
-    v.get_label_by_id('10').set_text(str(inp_exc_loci))
-    v.get_label_by_id('01').set_text(str(cmp_exc_loci))
-    v.get_label_by_id('11').set_text(str(intersection_loci))
+    v.get_label_by_id('10').set_text('')
+    v.get_label_by_id('01').set_text('')
+    v.get_label_by_id('11').set_text('')
+    
+    plt.annotate(str(inp_exc_loci), xy = v.get_label_by_id('10').get_position(), xytext = (0,-10), size = 'x-large',
+                ha = 'center', textcoords = 'offset points')
+    plt.annotate(str(cmp_exc_loci), xy = v.get_label_by_id('01').get_position(), xytext = (0,-10), size = 'x-large',
+                ha = 'center', textcoords = 'offset points')
+    plt.annotate(str(intersection_loci), xy = v.get_label_by_id('11').get_position(), xytext = (0,-10), size = 'x-large',
+                ha = 'center', textcoords = 'offset points')
     
     v.get_label_by_id('A').set_text('')
     v.get_label_by_id('B').set_text('')
@@ -316,11 +332,18 @@ def generate_venn(venn_data, colors, is_ref, ref_species, proj_species, reciproc
      
     plt.annotate('Compara', xy = v.get_label_by_id('01').get_position(), xytext = (30,-70), size = 'x-large',
                 ha = 'center', textcoords = 'offset points', bbox = dict(boxstyle = 'round, pad = 0.5', fc = colors[4], alpha = 0.3))
-    
-    plt.title('Overlap of ' + ref_species + (' reference ' if not is_ref else ' projection ') + 'loci (' + str(union_loci) + ' total)\nbetween Inparanoid super-clusters and Compara orthology data,\ngiven ' + str(reciprocal_id) + '% Compara reciprocal identity' + (', high-confidence only' if confidence else ''))
 
-    plt.show()
+    plt.title(ref_species + ' > ' + proj_species + (' reference ' if is_ref else ' projection ') + 'loci (' + str(union_loci) + ' total) coverage comparison\nbetween Inparanoid super-clusters and Compara orthology data,\ngiven ' + str(reciprocal_id) + '% Compara reciprocal identity' + (', high-confidence only' if confidence else ''))
+
+    if venn_output_path :
+        plt.savefig(venn_output_path + '/incomparanoid_' + ref_species.replace(' ','_') + '_2_' + proj_species.replace(' ','_') + '_recip_' 
+                        + str(reciprocal_id) + ('_all_confidence' if confidence else '') + ('_reference_loci' if is_ref else '_projection_loci') + '_comparison.png', 
+                    dpi=None, facecolor='w', edgecolor='w',
+                    orientation=None, papertype=None, format='png',
+                    transparent=True, bbox_inches=None, pad_inches=0.1,
+                    frameon=None)
 
+    plt.show()
 
 #----------------------------------------------------------------------------------------------------------------------
 # main
@@ -350,6 +373,7 @@ parser.add_argument('-g', '--generate_reactome_output', help='produce ortho_pair
 parser.add_argument('-R', '--reactome_gene_protein_path', help='output file containing gene::protein mappings for Reactome projection inference') # e.g. 'zmay_gene_protein_mapping.txt'
 parser.add_argument('-P', '--reactome_projection_path', help='output file containing reference::projection protein mappings for Reactome inference') # e.g. 'osat_zmay_mapping.txt'
 parser.add_argument('-V', '--venn_diagram', help='generate Venn diagram', action='store_true')
+parser.add_argument('-v', '--venn_output_path', help='save Venn diagrams to this directory')
 
 args = parser.parse_args()
 #print args
@@ -363,7 +387,7 @@ dict_inp_map = create_inp_map(args.inparanoid_input_path, dict_uniprot_map)
 dict_ens_map = create_ens_map(args.filtering_loci_path, args.ensembl_input_path, args.rap_map_path, args.reciprocal_id, dict_uniprot_map, 1 if args.confidence_high else 0)
 
 # generate stats and output them
-venn_data = compare_maps(dict_ens_map, dict_inp_map, args.comparison_file_path, args.ensembl_output_path, args.inparanoid_output_path)
+all_venn_data = compare_maps(dict_ens_map, dict_inp_map, args.comparison_file_path, args.ensembl_output_path, args.inparanoid_output_path)
 
 if args.generate_reactome_output == 'ensembl' :
     write_reactome_files(dict_ens_map, args.reactome_gene_protein_path, args.reactome_projection_path, args.projection_prefix)
@@ -372,8 +396,8 @@ if args.generate_reactome_output == 'inparanoid' :
 
 # NOTE: requires local matplotlib backend configuration
 if args.venn_diagram :
-    generate_venn(venn_data, ['red', 'yellow', 'orange', 'purple', 'lime'], 0, args.ref_species, args.proj_species, args.reciprocal_id, 1 if args.confidence_high else 0)
-    generate_venn(venn_data, ['green', 'yellow', 'lightgreen', 'purple', 'lime'], 1, args.ref_species, args.proj_species, args.reciprocal_id, 1 if args.confidence_high else 0)
+    generate_venn(all_venn_data[0], ['red', 'yellow', 'orange', 'blue', 'lime'], 1, args.ref_species, args.proj_species, args.reciprocal_id, 1 if args.confidence_high else 0, args.venn_output_path)
+    generate_venn(all_venn_data[1], ['green', 'yellow', 'lightgreen', 'blue', 'lime'], 0, args.ref_species, args.proj_species, args.reciprocal_id, 1 if args.confidence_high else 0, args.venn_output_path)
 
 #----------------------------------------------------------------------------------------------------------------------
 # end