Mercurial > repos > bornea > apostl_static_bubblegraph_generator
changeset 16:0a740024e014 draft
Uploaded
| author | bornea |
|---|---|
| date | Wed, 11 May 2016 11:14:37 -0400 |
| parents | 651a602e0c7f |
| children | aa0debcd27be |
| files | APOSTL_Static_Bubblegraph_Generator.py |
| diffstat | 1 files changed, 24 insertions(+), 7 deletions(-) [+] |
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--- a/APOSTL_Static_Bubblegraph_Generator.py Wed May 11 11:00:59 2016 -0400 +++ b/APOSTL_Static_Bubblegraph_Generator.py Wed May 11 11:14:37 2016 -0400 @@ -35,7 +35,7 @@ list_file = sys.argv[1] prey_file = sys.argv[2] crapome = sys.argv[3] -inter_file = sys.arg[4] +inter_file = sys.argv[4] main_x = sys.argv[5] main_y = sys.argv[6] size_id = sys.argv[7] @@ -50,7 +50,7 @@ outline_color = sys.argv[16] filt_color =sys.argv[17] outfile = sys.argv[18] -ins_path = sys.argv[15] +ins_path = "/home/bornea/galaxy_moffitt_dev/tools/Moffitt_Tools" if crapome == "None": crapome = "FALSE" @@ -73,10 +73,27 @@ if filt_color == "None": filt_color = "tan" -if label == "false": - label = "FALSE" -elif label == "true": - label = "TRUE" +if main_x == "lnNSAF": + main_x = "\"ln(NSAF)\"" +if main_y == "lnNSAF": + main_y = "\"ln(NSAF)\"" +if size_id == "lnNSAF": + size_id = "\"ln(NSAF)\"" + +if main_x == "log2FoldChange": + main_x = "\"log2(FoldChange)\"" +if main_y == "log2FoldChange": + main_y = "\"log2(FoldChange)\"" +if size_id == "log2FoldChange": + size_id = "\"log2(FoldChange)\"" + +if main_x == "logOddsScore": + main_x = "\"log(OddsScore)\"" +if main_y == "logOddsScore": + main_y = "\"log(OddsScore)\"" +if size_id == "logOddsScore": + size_id = "\"log(OddsScore)\"" + 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" " @@ -84,7 +101,7 @@ + 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('./BubbleGraph.png') os.rename('BubbleGraph.png', str(outfile))