plotHic2: plots HiC interaction matrix
In PhanstielLab/Sushi: Tools for visualizing genomics data

plots HiC interaction matrix

plotHic2(hicdata, chrom, chromstart, chromend, max_dist = 1e+05,
  zrange = NULL, palette = SushiColors(7), flip = FALSE,
  format = "auto", labeltype = "bin", resolution = NULL,
  plottype = "triangle")

`hicdata`	interaction matrix representing HiC data. Row and column names should be postions along a chromosome
`chrom`	chromosome of region to be plotted
`chromstart`	start position
`chromend`	end position
`max_dist`	The maximum distance of interaction to plot
`zrange`	The range of interaction scores to plot (more extreme value will be set to the max or min)
`palette`	color palette to use for representing interaction scores
`flip`	TRUE/FALSE whether plot should be flipped over the x-axis
`format`	The input format of the HiC data. Options are "sparse" (all data in first 3 colums) or "full" (large matrix)
`labeltype`	options are "bin" or "bp"
`resolution`	the width in bp of each pixel
`plottype`	options are "triangle" or "square"

data(Sushi_HiC.matrix)

chrom            = "chr11"
chromstart       = 500000
chromend         = 5050000

phic = plotHic(Sushi_HiC.matrix,chrom,chromstart,chromend,max_y = 20,zrange=c(0,28),palette = topo.colors,flip=FALSE)

labelgenome(chrom,chromstart,chromend,side=1,scipen=20,n=4,scale="Mb",edgeblankfraction=0.20,line=.18,chromline=.5,scaleline=0.5)

addlegend(phic[[1]],palette=phic[[2]],title="score",side="right",bottominset=0.4,topinset=0,xoffset=-.035,labelside="left",width=0.025,title.offset=0.035)