Plot Hi-C data with loops colored by community assignment.

If a vector of starts and ends is provided, one page will be generated per region.

Usage

plotHicCommunities(
  pdfName,
  communities,
  hicFile,
  norm = "SCALE",
  chroms,
  starts,
  ends,
  zmax,
  colorPalette
)

pdfName: a character string giving the file path. See the `file` parameter in `pdf()` for more information.
communities: GInteractions object containing loops to plot and a column called `loopCommunity` containing community assignments
hicFile: path to .hic file to plot
chroms: chromosome(s) of the region(s) to plot
starts: starting genomic location(s) of the region(s) to plot
ends: ending genomic location(s) of the region(s) to plot
zmax: a numeric value specifying the maximum range of hic scores to plot, where values greater than `zmax` will be set to`zmax`
colorPalette: a function corresponding to a color palette