hicPlotAverage regions plots the data computed by hicAverageRegions. It shows the summed up and averaged regions around all given reference points. This is useful to determine the difference between samples if the TAD configuration is equal or changed.

usage: hicPlotAverageRegions --matrix MATRIX --outputFile OUTPUTFILE [--log1p]
                             [--log] [--colorMap COLORMAP] [--vMin VMIN]
                             [--vMax VMAX] [--dpi DPI] [--help] [--version]

Required arguments

--matrix, -m

The averaged regions file computed by hicAverageRegions, ends npz.

--outputFile, -o

The averaged regions plot.

Optional arguments


Plot the log1p of the matrix values.

Default: False


Plot the 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: “hot_r”


Minimum score value.


Maximum score value.


Resolution for the image in case theouput is a raster graphics image (e.g png, jpg).

Default: 300


show program’s version number and exit

See hicAverageRegions for an example usage.