diff --git a/README.rst b/README.rst index a81115f..fc8deb4 100644 --- a/README.rst +++ b/README.rst @@ -86,7 +86,7 @@ If you have `git` installed, use this: git clone https://bitbucket.org/CBGR/intervene.git cd intervene - python setup.py install + python setup.py sdist install Install development version from `GitHub` ----------------------------------------- @@ -96,7 +96,7 @@ If you have `git` installed, use this: git clone https://github.com/asntech/intervene.git cd intervene - python setup.py install + python setup.py sdist install How to use Intervene ==================== diff --git a/docs/install.rst b/docs/install.rst index 99fc653..422b5c7 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -82,7 +82,7 @@ If you have `git` installed, use this: git clone https://bitbucket.org/CBGR/intervene.git cd intervene - python setup.py install + python setup.py sdist install diff --git a/docs/modules.rst b/docs/modules.rst index 6e31377..3b95149 100644 --- a/docs/modules.rst +++ b/docs/modules.rst @@ -50,6 +50,7 @@ This will save the results in the current working directory with a folder named "-o, --output","Output folder path where results will be stored. Default is current working directory." "--figtype","{pdf,svg,ps,tiff,png} Figure type for the plot. e.g. --figtype svg. Default is ``pdf``" "--figsize","Figure size as width and height.e.g. --figsize 12 12." + "--fontsize","Font size for the plot labels. Default is ``14``" "--dpi","Dots-per-inch (DPI) for the output. Default is: ``300``" "--fill","{number,percentage} Report number or percentage of overlaps (Only if --type=list). Default is ``number``" "--test","This will run the program on test data." diff --git a/intervene/intervene b/intervene/intervene index 2d95b04..68d9ccb 100755 --- a/intervene/intervene +++ b/intervene/intervene @@ -64,7 +64,11 @@ def main(): 'e.g. --figtype svg. Default is "%(default)s"\n\n') venn_parser.add_argument('--figsize', nargs=2, type=int, default=(12,12), help='Figure size as width and height.' - 'e.g. --figsize 12 12.\n\n') + 'e.g. --figsize 12 12.\n\n') + venn_parser.add_argument('--fontsize', dest='fontsize', type=int, default=14, + help='Font size for the plot labels.' + 'Default is: "%(default)s"\n\n') + venn_parser.add_argument('--dpi', type=int, default=300, help='Dots-per-inch (DPI) for the output. ' 'Default is: "%(default)s"\n\n') @@ -408,12 +412,12 @@ def main(): #create an RScript upset.create_r_script(labels, label_names, options) else: - fig, ax = list_venn.venn2(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn2(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #else input considered as bed file else: labels = upset.genomic_upset(options.input) - fig, ax = list_venn.venn2(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn2(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #fig, ax = genomic_venn.venn2(input_files=options.input, # options=options, names=label_names, plot_type=plot_type) @@ -438,11 +442,11 @@ def main(): upset.create_r_script(labels, label_names, options) else: - fig, ax = list_venn.venn3(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn3(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #else input considered as bed file else: labels = upset.genomic_upset(options.input) - fig, ax = list_venn.venn3(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn3(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #fig, ax = genomic_venn.venn3(input_files=options.input, options=options, names=label_names, plot_type=plot_type) @@ -468,12 +472,12 @@ def main(): upset.create_r_script(labels, label_names, options) else: - fig, ax = list_venn.venn4(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn4(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #else input considered as bed file else: labels = upset.genomic_upset(options.input) - fig, ax = list_venn.venn4(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn4(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #fig, ax = genomic_venn.venn4(input_files=options.input, options=options, names=label_names, plot_type=plot_type) @@ -501,11 +505,11 @@ def main(): upset.create_r_script(labels, label_names, options) else: - fig, ax = list_venn.venn5(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn5(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #else input considered as genomic regions file else: labels = upset.genomic_upset(options.input) - fig, ax = list_venn.venn5(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn5(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #fig, ax = genomic_venn.venn5(input_files=options.input, options=options, names=label_names, plot_type=plot_type) elif helpers.venn_order(options.input) == 6: @@ -532,12 +536,12 @@ def main(): #create an RScript upset.create_r_script(labels, label_names, options) else: - fig, ax = list_venn.venn6(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn6(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #else input considered as bed file else: labels = upset.genomic_upset(options.input) - fig, ax = list_venn.venn6(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize) + fig, ax = list_venn.venn6(labels, names=label_names, dpi=options.dpi, colors=options.colors, figsize=options.figsize, fontsize=options.fontsize) #fig, ax = genomic_venn.venn6(input_files=options.input,options=options, names=label_names, plot_type=plot_type) else: