starting to work with genes reseived from the find_exons

visualize.py

@@ -62,17 +62,20 @@ def make_box_plot(group1, group2, gene_names, scores, output_directory, figure_n
 	group_one = []
 	group_two = []
 
-	for name in group1:
-		group_one.append(scores[gene_names.index(name)])
+	#for name in group1:
+	#	group_one.append(scores[gene_names.index(name)])
 
-	for name in group2:
-		group_two.append(scores[gene_names.index(name)])
+	#for name in group2:
+	#	group_two.append(scores[gene_names.index(name)])
 
 	#plt.figure()
 	#plt.boxplot([group_one, group_two])
 
-	groups_names = ['Important in ED', 'Not important in ED']
+	groups_names = ['gen1', 'gen2']
 
+	#data = [group_one, group_two]
+	group_one = [2]
+	group_two = [8, 6]
 	data = [group_one, group_two]
 
 	fig, ax1 = plt.subplots(figsize=(10,10))
@@ -92,11 +95,11 @@ def make_box_plot(group1, group2, gene_names, scores, output_directory, figure_n
 	#ax1.set_axisbelow(True)
 
 	ax1.set_title('The visualization of correlation between gene and exons length')
-	ax1.set_xlabel('Groups')
-	ax1.set_ylabel('Number')
+	ax1.set_xlabel('Genen')
+	ax1.set_ylabel('Scores')
 
 	#ax1.set_ylim(bottom, top)
-	ax1.set_xticklabels(np.repeat(groups_names, 2), rotation=45, fontsize=8)
+	ax1.set_xticklabels(np.repeat(groups_names, 5), rotation=45, fontsize=8) #something is failing with this annotation
 
 
 	plt.show()
@@ -150,6 +153,7 @@ def make_reg_plot(x_array, y_array, gene_names, output_directory, figure_name, c
 
 def read_correlation(correlation_file):
 	gene_names = []
+	#transcript_names = []
 	scores = []
 	gene_lengths = []
 	exons_lengths = []
@@ -158,6 +162,10 @@ def read_correlation(correlation_file):
 			if not cor_line.startswith('#'):
 				cor_line_array = re.split(r'\t', cor_line.rstrip('\n'))
 				gene_names.append(cor_line_array[0])
+				#transcript_names.append(cor_line_array[1])
+				#scores.append(float(cor_line_array[2]))
+				#gene_lengths.append(int(cor_line_array[3]))
+				#exons_lengths.append(int(cor_line_array[4]))
 				scores.append(float(cor_line_array[1]))
 				gene_lengths.append(int(cor_line_array[2]))
 				exons_lengths.append(int(cor_line_array[3]))