hicPlotAverageRegions

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

--log1p

Plot the log1p of the matrix values.

Default: False

--log

Plot the 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: “hot_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: 300

--version

show program’s version number and exit

See hicAverageRegions for an example usage.