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Last data update: 2014.03.03

R: plots HiC interactio matrix

plotHic

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Sushi)
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Sushi/plotHic.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotHic
> ### Title: plots HiC interactio matrix
> ### Aliases: plotHic
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>