plotHic {Sushi} | R Documentation |
plots HiC interactio matrix
plotHic(hicdata, chrom, chromstart, chromend, max_y = 30, zrange = NULL, palette = SushiColors(7), flip = FALSE)
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 |
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)