def on_button_go_plot_clicked(self, widget): """ 04-19-05 06-14-05 use graphDotOutput() and insert it into the textbuffer 10-11-05 add cluster_id and go_no for each graph """ if self.cluster == None: print "Cluster not loaded in" return #first construct the graph subgraph = self.cluster_info_instance.graph_from_node_edge_set(\ self.cluster.vertex_set, self.cluster.edge_set) pathlist = [] treeselection_go_association = self.treeview_go_association.get_selection() treeselection_go_association.selected_foreach(foreach_cb, pathlist) if len(pathlist) >0: for i in range(len(pathlist)): go_no = self.liststore_go_association[pathlist[i][0]][0] graphSrcFname = '/tmp/GuiAnalyzer.dot' graphFname = '/tmp/GuiAnalyzer.ps' graphSrcF = open(graphSrcFname, 'w') graphDotOutput(graphSrcF, subgraph, \ self.gene_no2gene_id, self.gene_no2go_no, \ function=int(go_no), weighted=0) graphSrcF.close() #06-14-05 get the plot_type_command from the comboboxentry_plot_type entry = self.comboboxentry_plot_type.child plot_type_command = entry.get_text() if plot_type_command=='neato' or plot_type_command=='twopi': plot_type_command += ' -Goverlap=false' #06-14-05 -Goverlap=false passed to neato or twopi commandline = '%s -Tps %s -o %s'%(plot_type_command, graphSrcFname, graphFname) system_call(commandline) #10-11-05 temporary adding this block to draw pictures in png format outputfname = '/tmp/%s_%s.png'%(self.cluster.cluster_id, go_no) commandline = '%s -Tpng %s -o %s'%(plot_type_command, graphSrcFname, outputfname) system_call(commandline) textbuffer = self.textview_subgraph.get_buffer() im = Image.open(graphFname) ar = fromimage(im) pixbuf = gtk.gdk.pixbuf_new_from_array(ar, gtk.gdk.COLORSPACE_RGB, 8) startiter = textbuffer.get_start_iter() textbuffer.insert_pixbuf(startiter, pixbuf) startiter = textbuffer.get_start_iter() textbuffer.insert(startiter, "cluster_id:%s go_no:%s"%(self.cluster.cluster_id, go_no)) #cleanup the temporary files and others del im del ar
def output_p_gene_id_list(self, curs, schema_instance1, schema_instance2, p_gene_id_list, writer, pic_output_dir,\
pga_instance1, pga_instance2, cluster_info_instance, simple):
"""
10-15-05
add score1 and is_accepted1
10-17-05
score and is_accepted depend on whether pga_instance is None or not
10-17-05 add simple to allow no graph pictures output
also get prediction from schema_instance1 and calculate the score if prediction is available
10-18-05
sort the p_gene_id_list first
"""
#10-15-05 following sentence slightly different from PredictionFilterByClusterSize.py in the trailing edge_gradient
#and d_matrix is a placeholder
sql_sentence1 = "SELECT p.p_gene_id, p.gene_no, p.go_no, p.is_correct, p.is_correct_l1, \
p.is_correct_lca, p.avg_p_value, p.no_of_clusters, p.cluster_array, p.p_value_cut_off, p.recurrence_cut_off, \
p.connectivity_cut_off, p.cluster_size_cut_off, p.unknown_cut_off, p.depth_cut_off, p.mcl_id, p.lca_list, \
p.vertex_gradient, p.edge_gradient, m.vertex_set, s.edge_set, 'd_matrix', 'r' from %s p, %s s, %s m where \
p.mcl_id=s.splat_id and p.mcl_id=m.mcl_id"%(schema_instance1.p_gene_table, \
schema_instance1.splat_table, schema_instance1.mcl_table)
sql_sentence2 = "SELECT p.p_gene_id, p.gene_no, p.go_no, p.is_correct, p.is_correct_l1, \
p.is_correct_lca, p.avg_p_value, p.no_of_clusters, p.cluster_array, p.p_value_cut_off, p.recurrence_cut_off, \
p.connectivity_cut_off, p.cluster_size_cut_off, p.unknown_cut_off, p.depth_cut_off, p.mcl_id, p.lca_list, \
p.vertex_gradient, p.edge_gradient, m.vertex_set, s.edge_set, 'd_matrix', 'r' from %s p, %s s, %s m where \
p.mcl_id=s.splat_id and p.mcl_id=m.mcl_id"%(schema_instance2.p_gene_table, \
schema_instance2.splat_table, schema_instance2.mcl_table)
writer.writerow(['p_gene_id', 'gene_no', 'go_no', 'is_correct_lca', 'p_value', 'recurrence', 'connectivity',\
'cluster_size', 'unknown_ratio', 'mcl_id', 'lca_list', 'edge_gradient', 'score1', 'is_accepted1', 'score2', 'is_accepted2'])
p_gene_id_list.sort()
for p_gene_id in p_gene_id_list:
#sql_sentence1's prediction infomation is not gonna be displayed
curs.execute("%s and p.p_gene_id=%s"%(sql_sentence1, p_gene_id))
rows = curs.fetchall()
if rows:
p_attr_instance1 = prediction_attributes(rows[0], type=3)
else:
p_attr_instance1 = None
#sql_sentence2's prediction infomation is going to be displayed
curs.execute("%s and p.p_gene_id=%s"%(sql_sentence2, p_gene_id))
rows = curs.fetchall()
if rows:
p_attr_instance2 = prediction_attributes(rows[0], type=3)
if pga_instance1 and p_attr_instance1:
(is_accepted1, score1) = pga_instance1.prediction_accepted(p_attr_instance1.go_no, \
[-math.log(p_attr_instance1.p_value_cut_off), p_attr_instance1.recurrence_cut_off, \
p_attr_instance1.connectivity_cut_off, p_attr_instance1.cluster_size_cut_off, \
p_attr_instance1.edge_gradient])
else:
is_accepted1, score1 = None, None
if pga_instance2:
(is_accepted2, score2) = pga_instance2.prediction_accepted(p_attr_instance2.go_no, \
[-math.log(p_attr_instance2.p_value_cut_off), p_attr_instance2.recurrence_cut_off, \
p_attr_instance2.connectivity_cut_off, p_attr_instance2.cluster_size_cut_off, \
p_attr_instance2.edge_gradient])
else:
is_accepted2, score2 = None, None
writer.writerow([p_attr_instance2.p_gene_id, p_attr_instance2.gene_no, p_attr_instance2.go_no, \
p_attr_instance2.is_correct_lca, p_attr_instance2.avg_p_value, p_attr_instance2.recurrence_cut_off,\
p_attr_instance2.connectivity_cut_off, p_attr_instance2.cluster_size_cut_off, p_attr_instance2.unknown_cut_off,\
p_attr_instance2.mcl_id, p_attr_instance2.lca_list, p_attr_instance2.edge_gradient, score1, is_accepted1, \
score2, is_accepted2])
if not simple:
#prepare vertex_set and edge_set to draw graphs
vertex_set = p_attr_instance2.vertex_set[1:-1].split(',')
vertex_set = map(int, vertex_set)
edge_set = p_attr_instance2.edge_set[2:-2].split('},{')
for i in range(len(edge_set)):
edge_set[i] = edge_set[i].split(',')
edge_set[i] = map(int, edge_set[i])
#following copied from GuiAnalyzer.py
subgraph = cluster_info_instance.graph_from_node_edge_set(vertex_set, edge_set)
graphSrcFname = '/tmp/GuiAnalyzer.dot'
graphFname = os.path.join(pic_output_dir, '%s_%s_%s_%s.png'%(p_attr_instance2.p_gene_id, \
p_attr_instance2.gene_no, p_attr_instance2.go_no, p_attr_instance2.mcl_id))
graphSrcF = open(graphSrcFname, 'w')
graphDotOutput(graphSrcF, subgraph, \
self.gene_no2gene_id, self.gene_no2go_no, \
centralnode=p_attr_instance2.gene_no, function=p_attr_instance2.go_no, weighted=0, )
graphSrcF.close()
plot_type_command='neato -Goverlap=false'
commandline = '%s -Tpng %s -o %s'%(plot_type_command, graphSrcFname, graphFname)
system_call(commandline)
