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.
`–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 not shown as 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.

../../../_images/hicPlotMatrix_perChromosome.png

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