TripleColumn (-tri) : a boolean if input file is from HiC-Pro pipeline.ĭark (-da) : a boolean to use black background for the output.īedFile (-bed) : a file name for bin annotations, if -tri parameter is set. Verbose (-v) : print version and arguments into a file. Output (-o) : prefix for the output file. Name (-n) : a list of labels for the experiment. Contentsįor reading more about each parameter, please check the manual.įiles (-f) : a list of filenames to be plotted. HiCPlotter is purposefully designed with the least amount of dependencies to make it easily applicable. HiCPlotter is tested on Mac OS (Mountain Lion and Yosemite) and Linux (RedHat 4.1.2-44 and 5.5-Final) systems. If you receive error(s) related to one or more of these modules, check this solution and/or check versions of python and required modules.Please note: scipy, numpy and matplotlib modules should be installed and updated to current version.
Python HiCPlotter.py -f HUVEC.txt NHEK.txt -r 25000 -chr chr16 -n HUVEC NHEK -da 1 -o TOX3 -mm 6 -spi 1 -t -tl States States -s 1940 -e 2156 -hist, , -hl H3K9me3,CTCF H3K9me3,CTCF -si 1 -hc FF78B7,85d8e6 FF78B7,85d8e6 -fhist 1,0 1,0 -hm 18,600 18,600 -c 1 -a -al Domains Domains -ac cecece cecece -g