hicPlotMatrix

Creates a Heatmap of a HiC matrix.

usage: hicPlotMatrix --matrix MATRIX --outFileName OUTFILENAME [--title TITLE]
                     [--scoreName SCORENAME] [--perChromosome]
                     [--clearMaskedBins]
                     [--chromosomeOrder CHROMOSOMEORDER [CHROMOSOMEORDER ...]]
                     [--region REGION] [--region2 REGION2] [--log1p] [--log]
                     [--colorMap COLORMAP] [--vMin VMIN] [--vMax VMAX]
                     [--dpi DPI] [--bigwig BIGWIG] [--flipBigwigSign]
                     [--scaleFactorBigwig SCALEFACTORBIGWIG] [--help]
                     [--version]

Required arguments

–matrix, -m	Path of the Hi-C matrix to plot.
–outFileName, -out
	File name to save the image.

Optional arguments

–title, -t	Plot title.
–scoreName, -s
	Score name label for the heatmap legend.
–perChromosome
	Instead of plotting the whole matrix, each chromosome is plotted next to the other. This parameter is not compatible with –region. Default: False
–clearMaskedBins
	If set, masked bins are removed from the matrix and the nearest bins are extended to cover the empty space instead of plotting black lines. Default: False
–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	Plot the log1p of the matrix values. Default: False
–log	Plot the MINUS log of the matrix values. Default: False
–colorMap	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	Minimum score value.
–vMax	Maximum score value.
–dpi	Resolution for the image in case theouput is a raster graphics image (e.g png, jpg). Default: 72
–bigwig	Bigwig file to plot below the matrix. This can for example be used to visualize A/B compartments or ChIP-seq data.
–flipBigwigSign
	The sign of the bigwig values are flipped. Useful if hicPCA gives inverted values. Default: False
–scaleFactorBigwig
	Scale the values of a bigwig file by the given factor. Default: 1.0
–version	show program’s version number and exit

Details

hicplotMatrix takes a Hi-C matrix and plots the interactions of all or some chromosomes.

Examples

Here’s an example of Hi-C data from wild-type D. melanogaster embryos.

This plot shows contacts of a Hi-C matrix that was merged to a 25 kb bin size using hicMergeMatrixBins. Alternatively, chromosomes can be plotted separately.

$ hicPlotMatrix -m Dmel.h5 -o hicPlotMatrix.png \
-t 'D.melanogaster (--perChromosome)' --log1p \
--clearMaskedBins --chromosomeOrder 2L 2R 3L 3R X --perChromosome