hicPlotMatrix

Creates a Heatmap of a Hi-C 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.
--perChromosome=False
 Instead of plotting the whole matrix, each chromosome is plotted next to the other. This parameter is not compatible with –region
--clearMaskedBins=False
 if set, masked bins are removed from the matrix
--whatToShow=heatmap
 

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

Possible choices: heatmap, 3D, both

--chromosomeOrder
 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.
--colorMap=RdYlBu_r
 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