Plots the number of interactions around a given reference point in a region.

usage: hicPlotViewpoint --matrix MATRIX [MATRIX ...] --region REGION
                        --outFileName OUTFILENAME --referencePoint
                        REFERENCEPOINT [--chromosome CHROMOSOME]
                        [--interactionOutFileName INTERACTIONOUTFILENAME]
                        [--dpi DPI] [--version] [--help]

Required arguments

--matrix, -m

Hi-C matrix to plot.


The format is chr:start-end.

--outFileName, -o

File name of the image to save.

--referencePoint, -rp

Reference point. Needs to be in the format: ‘chr:100’ for a single reference point or ‘chr:100-200’ for a reference region.

Optional arguments

--chromosome, -C

Optional parameter: Only show results for this chromosome.

--interactionOutFileName, -i

Optional parameter: If set, a bedgraph file with all interaction will be created.


Optional parameter: Resolution for the image in case theouput is a raster graphics image (e.g png, jpg) (Default: 300).

Default: 300


show program’s version number and exit