plotHic: plots HiC interactio matrix

In Sushi: Tools for visualizing genomics data

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)

Example output

Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: biomaRt

Sushi documentation built on Nov. 8, 2020, 7:48 p.m.