- pybedtools.contrib.venn_maker.venn_maker(beds, names=None, figure_filename=None, script_filename=None, additional_args=None, run=False)¶
Given a list of interval files, write an R script to create a Venn diagram of overlaps (and optionally run it).
The R script calls the venn.diagram function of the R package VennDiagram for extremely flexible Venn and Euler diagram creation. Uses
cleaned_intersect()to create string representations of shared intervals.
bedsis a list of up to 4 filenames or BedTools.
namesis a list of names to use for the Venn diagram, in the same order as
beds. Default is “abcd”[:len(beds)].
figure_filenameis the TIFF file to save the figure as.
script_filenameis the optional filename to write the R script to
additional_argsis list that will be inserted into the R script, verbatim. For example, to use scaled Euler diagrams with different colors, use:
additional_args = ['euler.d=TRUE', 'scaled=TRUE', 'cat.col=c("red","blue")']
runis True, then assume R is installed, is on the path, and has VennDiagram installed … and run the script. The resulting filename will be saved as