This program makes a distance vs. hi-c counts plots. It can use several matrix files to compare them. If the –perchr option is given, each chromosome is plotted independently. In the case of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple matrices denser matrices are scaled down to match the sum of the smaller matrix.

usage: hicPlotDistVsCounts [-h] --matrices MATRICES [MATRICES ...]
                           [--labels LABELS [LABELS ...]] [--skipDiagonal]
                           --plotFile file name [--maxdepth INT bp] [--perchr]
                           [--chromosomeExclude CHROMOSOMEEXCLUDE [CHROMOSOMEEXCLUDE ...]]
                           [--outFileData OUTFILEDATA]
                           [--plotsize PLOTSIZE PLOTSIZE] [--version]
optional arguments
--matrices, -m HiC normalized (corrected) matrices. Each path should be separated by a space.
--labels Label to assign to each matrix file. Each label should be separated by a space. Quote labels that contain spaces: E.g. –labels label1 “labels 2”. If no labels are given then the file name is used.
--skipDiagonal=False, -s=False
 If set, diagonal counts are not included
--plotFile, -o File name to save the file. The given file ending will be used to determine the image format. The available options are: .png, .emf, .eps, .pdf and .svg.
 Maximum distance from diagonal to use. In other words, distances up to maxDeph arecomputed. Default is 3 million bp.
--perchr=False generate plots per chromosome. If more than one HiC matrix is given to `–matrices` thenfor each chromosome a new plot is made. Otherewise, a single plot with one line perchromosome is created
 Exclude the given list of chromosomes. This is useful for example to exclude the Y chromosome. The names of the chromosomes should be separated by space
--outFileData If given, the data underlying the plots is saved on this file
--plotsize width and height of the plot (in inches). Default is 6*number of cols, 4 * number of rows. The maximum number of rows is 4. Example –plotsize 6 5
--version show program’s version number and exit