Sushi (version 1.10.0)

plotHic: plots HiC interactio matrix

Description

plots HiC interactio matrix

Usage

plotHic(hicdata, chrom, chromstart, chromend, max_y = 30, zrange = NULL, palette = SushiColors(7), flip = FALSE)

Arguments

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_y

The maximum bin distance 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

Examples

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)