changeset 11:8f463e2a34d5 draft

Uploaded

--- a/APOSTL_Static_Bubblegraph_Generator.py	Tue Mar 15 15:19:47 2016 -0400
+++ b/APOSTL_Static_Bubblegraph_Generator.py	Wed May 11 10:59:06 2016 -0400
@@ -35,46 +35,56 @@
 list_file = sys.argv[1]
 prey_file = sys.argv[2]
 crapome = sys.argv[3]
-color = sys.argv[4]
-label = sys.argv[5]
-cutoff = sys.argv[6]
-mq_sc = sys.argv[7]
-inc_file = sys.argv[8]
-exc_file = sys.argv[9]
-output_file_name = sys.argv[10]
-bub_zoom_NSAF = sys.argv[11]
-bub_zoom_SAINT =sys.argv[12]
-bub_SAINT = sys.argv[13]
-bub_NSAF = sys.argv[14]
+inter_file = sys.arg[4]
+main_x = sys.argv[5]
+main_y = sys.argv[6]
+size_id = sys.argv[7]
+color = sys.argv[8]
+SS_cutoff = sys.argv[9]
+FC_cutoff = sys.argv[10]
+NS_cutoff = sys.argv[11]
+theme = sys.argv[12]
+label = sys.argv[13]
+label_color = sys.argv[14]
+bubble_color = sys.argv[15]
+outline_color = sys.argv[16]
+filt_color =sys.argv[17]
+outfile = sys.argv[18]
 ins_path = sys.argv[15]
 
 if crapome == "None":
 	crapome = "FALSE"
 
+if color == "None":
+	color = "Tan"
+
+if theme == "None":
+	theme = "Default"
+
+if label_color == "None":
+	label_color = "black"
+
+if bubble_color == "None":
+	bubble_color = "Alizarin crimson"
+
+if outline_color == "None":
+	outline_color = "black"
+
+if filt_color == "None":
+	filt_color = "tan"
 
 if label == "false":
 	label = "FALSE"
 elif label == "true":
 	label = "TRUE" 
 
-cmd = (r"Rscript "+ str(ins_path) + r"/bubbles_v9_NSAF_natural_log.R " + str(list_file) + r" "
-    + str(prey_file) + r" " + str(crapome) + r" " + str(color) + r" " + str(label) + r" "
-    + str(cutoff) + r" " + str(mq_sc) + r" " + str(inc_file) + r" " + str(exc_file))
+cmd = (r"Rscript "+ str(ins_path) + r"/Static_Bubble_Plot_Cmdln.R " + str(list_file) + r" "
+    + str(prey_file) + r" " + str(crapome) + r" " + str(inter_file) + r" " + str(main_x) + r" " + str(main_y) + r" "
+    + str(size_id) + r" " + str(color) + r" " + str(SS_cutoff) + r" " + str(FC_cutoff) + r" " + str(NS_cutoff)
+    + r" " + str(theme) + r" " + str(label) + r" " + str(label_color) + r" " + str(bubble_color) + r" " + str(outline_color)
+    + r" " + str(filt_color))
 os.system(cmd)
 time.sleep(3)
 
-open('./output.txt')
-os.rename('output.txt', str(output_file_name))
-
-open('./bubble_zoom_NSAF.png')
-os.rename('bubble_zoom_NSAF.png', str(bub_zoom_NSAF))
-
-open('./bubble_zoom_SAINT.png')
-os.rename('bubble_zoom_SAINT.png', str(bub_zoom_SAINT))
-
-open('./bubble_SAINT.png')
-os.rename('bubble_SAINT.png', str(bub_SAINT))
-
-open('./bubble_NSAF.png')
-os.rename('bubble_NSAF.png', str(bub_NSAF))
-
+open('./BubbleGraph.png')
+os.rename('BubbleGraph.png', str(outfile))