Creates a Heatmap of a HiC matrix

usage: hicPlotMatrix [-h] --matrix MATRIX [--title TITLE]
                     [--scoreName SCORENAME] --outFileName OUTFILENAME
                     [--perChromosome] [--clearMaskedBins]
                     [--chromosomeOrder CHROMOSOMEORDER [CHROMOSOMEORDER ...]]
                     [--region REGION] [--region2 REGION2] [--log1p] [--log]
                     [--colorMap COLORMAP] [--vMin VMIN] [--vMax VMAX]
                     [--dpi DPI] [--pca PCA [PCA ...]] [--version]

Named 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

Default: False


if set, masked bins are removed from the matrix

Default: False

 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

Plot the log1p of the matrix values.

Default: False


Plot the MINUS log of the matrix values.

Default: False


Color map to use for the heatmap. Available values can be seen here: http://matplotlib.org/examples/color/colormaps_reference.html

Default: “RdYlBu_r”

–vMin vMin
–vMax vMax

Resolution for the image in case theouput is a raster graphics image (e.g png, jpg)

Default: 72

–pca List of eigenvector from pca analysis as bigwig or bedgraph files.
–version show program’s version number and exit