Creates a Heatmap of a HiC matrix

usage: hicPlotMatrix [-h] --matrix MATRIX [--title TITLE]
                     [--scoreName SCORENAME] --outFileName OUTFILENAME
                     [--perChromosome] [--clearMaskedBins]
                     [--whatToShow {heatmap,3D,both}]
                     [--chromosomeOrder CHROMOSOMEORDER [CHROMOSOMEORDER ...]]
                     [--region REGION] [--region2 REGION2] [--log1p] [--log]
                     [--colorMap COLORMAP] [--vMin VMIN] [--vMax VMAX]
                     [--zMax ZMAX] [--dpi DPI] [--version]
optional arguments
--matrix, -m Path of the Hi-C matrix to plot
--title, -t Plot title
--scoreName, -s
 Score name
--outFileName, -out
 File name to save the image.
 Instead of plotting the whole matrix, each chromosome is plotted next to the other. This parameter is not compatible with –region
 if set, masked bins are removed from the matrix

Options are: “heatmap”, “3D”, and “both”. Default is heatmap

Possible choices: heatmap, 3D, both

 Chromosomes and order in which the chromosomes should be plotted. This option overrides –region and –region2
--region Plot only this region. The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless –region2 is given
--region2 If given, then only the region defined by –region and –region2 is given. The format is the same as –region1
--log1p=False Plot the log1p of the matrix values.
--log=False Plot the *MINUS* log of the matrix values.
 Color map to use for the heatmap. Available values can be seen here: http://matplotlib.org/examples/color/colormaps_reference.html
--vMin vMin
--vMax vMax
--zMax zMax for 3D plot
--dpi=72 Resolution for the image in case theouput is a raster graphics image (e.g png, jpg)
--version show program’s version number and exit