plotHic {Sushi} | R Documentation

## 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)

[Package Sushi version 1.28.0 Index]