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] [--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.
–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.

../../_images/hicPlotMatrix.png

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