From e96beec2d79438e6ca60cee09325037779c6e1fc Mon Sep 17 00:00:00 2001 From: Chris Miller Date: Tue, 15 Jan 2019 15:28:16 -0600 Subject: [PATCH 1/2] rm sets.x.label and mainbar.y.label from R code These two params don't exist in the upset R package version that's packaged with intervene in Conda. Removing this fixes the problem. --- intervene/modules/upset/upset.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/intervene/modules/upset/upset.py b/intervene/modules/upset/upset.py index eb99463..fed06d0 100644 --- a/intervene/modules/upset/upset.py +++ b/intervene/modules/upset/upset.py @@ -195,7 +195,7 @@ def create_r_script(labels, names, options): else: options.showzero = "'on'" - temp_f.write('upset(fromExpression(expressionInput), nsets='+str(len(key))+', nintersects='+str(options.ninter)+', show.numbers="'+str(options.showsize)+'", main.bar.color="'+options.mbcolor+'", sets.bar.color="'+options.sbcolor+'", empty.intersections='+str(options.showzero)+', order.by = "'+options.order+'", number.angles = 0, mainbar.y.label ="'+options.mblabel+'", sets.x.label ="'+options.sxlabel+'")\n') + temp_f.write('upset(fromExpression(expressionInput), nsets='+str(len(key))+', nintersects='+str(options.ninter)+', show.numbers="'+str(options.showsize)+'", main.bar.color="'+options.mbcolor+'", sets.bar.color="'+options.sbcolor+'", empty.intersections='+str(options.showzero)+', order.by = "'+options.order+'", number.angles = 0)\n') temp_f.write('invisible(dev.off())\n') #print temp_f.read() @@ -288,4 +288,4 @@ def one_vs_rest_intersection(beds, peaks, output, **kwoptions): f.close() return matrix_file - \ No newline at end of file + From a0ae7e273ed2d2b52eee9150c089931fd37395c2 Mon Sep 17 00:00:00 2001 From: Chris Miller Date: Tue, 15 Jan 2019 15:32:04 -0600 Subject: [PATCH 2/2] remove mblabel and xlabel options they don't exist in the R package --- intervene/intervene | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/intervene/intervene b/intervene/intervene index 8d0f542..97fa43a 100755 --- a/intervene/intervene +++ b/intervene/intervene @@ -177,14 +177,7 @@ def main(): upset_parser.add_argument('--sbcolor', type=str, default='#317eab', help='Color of set size bar plot. ' 'Default is: "%(default)s".\n\n') - - upset_parser.add_argument('--mblabel', type=str, default='No. of Intersections', - help='The y-axis label of the intersection size bars. ' - 'Default is: "%(default)s".\n\n') - upset_parser.add_argument('--sxlabel', type=str, default='Set size', - help='The x-axis label of the set size bars. ' - 'Default is: "%(default)s".\n\n') - + upset_parser.add_argument('--figtype', dest="figtype",choices=('pdf','svg','ps','tiff','png'), default='pdf',help='Figure type for the plot. ' 'e.g. --figtype svg. Default is "%(default)s"\n\n')