hicPlotMatrix

Creates a heatmap of a Hi-C 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 [BIGWIG ...]]
                     [--bigwigAdditionalVerticalAxis]
                     [--vMinBigwig VMINBIGWIG] [--vMaxBigwig VMAXBIGWIG]
                     [--flipBigwigSign]
                     [--scaleFactorBigwig SCALEFACTORBIGWIG]
                     [--fontsize FONTSIZE] [--rotationX ROTATIONX]
                     [--rotationY ROTATIONY]
                     [--increaseFigureWidth INCREASEFIGUREWIDTH]
                     [--increaseFigureHeight INCREASEFIGUREHEIGHT]
                     [--loops LOOPS]
                     [--loopLargeRegionsOperation {first,last,center}]
                     [--tads TADS] [--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”).

Default: “RdYlBu_r”

--vMin

Minimum score value.

--vMax

Maximum score value.

--dpi

Resolution for the image in case theoutput is a raster graphics image (e.g png, jpg) (Default: 72).

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.

--bigwigAdditionalVerticalAxis

Add an additional axis to determine the values of a bigwig file in 2D better.

Default: False

--vMinBigwig

Minimum score value for bigwig.

--vMaxBigwig

Maximum score value for bigwig

--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).

Default: 1.0

--fontsize

Fontsize in the plot for x and y axis (Default: 10).

Default: 10

--rotationX

Rotation in degrees for the labels of x axis (Default: 0).

Default: 0

--rotationY

Rotation in degrees for the labels of y axis (Default: 0).

Default: 0

--increaseFigureWidth

Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this (Default: 0.5).

Default: 0.5

--increaseFigureHeight

Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this (Default: 0.5).

Default: 0.5

--loops

Bedgraph file to plot detected long range contacts from hicDetectLoops.

--loopLargeRegionsOperation

Possible choices: first, last, center

If a given coordinate in the bed file is larger than a bin of the input matrix, by default only the first bin is taken into account. However there are more possibilities to handel such a case. Users can ask for the last bin or for center of the region.

Default: “first”

--tads

Bedgraph file to plot detected tads

--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 all contacts of a Hi-C matrix. Its bins were merged into 25 kb bins 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