hicPlotAverage regions plots the data computed by hicAverageRegions. It shows the summed up and averaged regions around all given reference points. This tool is useful to plot differences at certain reference points as for example TAD boundaries between samples.

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 (npz file).

--outputFile, -o

The averaged regions plot.

Optional arguments


Plot log1p of the matrix values.

Default: False


Plot 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”).

Default: “hot_r”


Minimum score value.


Maximum score value.


Resolution of image ifouput is a raster graphics image (e.g png, jpg) (Default: 300).

Default: 300


show program’s version number and exit

See hicAverageRegions for an example usage.