Creates a Heatmap of a HiC matrix.

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

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.

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 and the nearest bins are extended to cover the empty space instead of plotting black lines.

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 Minimum score value.
–vMax Maximum score value.

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.

The sign of the bigwig values are flipped. Useful if hicPCA gives inverted values.

Default: False


Scale the values of a bigwig file by the given factor.

Default: 1.0

–version show program’s version number and exit


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


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