hicPlotViewpoint¶
Plots the number of interactions around a given reference point in a region.
usage: hicPlotViewpoint --matrix MATRIX [MATRIX ...] --region REGION
--outFileName OUTFILENAME --referencePoint
REFERENCEPOINT [--chromosome CHROMOSOME]
[--interactionOutFileName INTERACTIONOUTFILENAME]
[--dpi DPI] [--version] [--help]
Required arguments¶
–matrix, -m | path of the Hi-C matrices to plot |
–region | The format is chr:start-end |
–outFileName, -o | |
File name to save the image. | |
–referencePoint, -rp | |
Reference point. Needs to be in the format: ‘chr:100’ for a single reference point or ‘chr:100-200’ for a reference region. |
Optional arguments¶
–chromosome, -C | |
Optional parameter: Only show results for this chromosome. | |
–interactionOutFileName, -i | |
Optional parameter: If set a bedgraph file with all interaction will be created. | |
–dpi | Optional parameter: 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 |