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
Hi-C matrix to plot.
- --region
The format is chr:start-end.
- --outFileName, -o
File name of the imapge to save.
- --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