plotHic2: plots HiC interaction matrix

Description Usage Arguments Examples

View source: R/plotHic2.R

Description

plots HiC interaction matrix

Usage

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plotHic2(hicdata, chrom, chromstart, chromend, max_dist = 1e+05,
  zrange = NULL, palette = SushiColors(7), flip = FALSE,
  format = "auto", labeltype = "bin", resolution = NULL,
  plottype = "triangle")

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_dist

The maximum distance of interaction 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

format

The input format of the HiC data. Options are "sparse" (all data in first 3 colums) or "full" (large matrix)

labeltype

options are "bin" or "bp"

resolution

the width in bp of each pixel

plottype

options are "triangle" or "square"

Examples

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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)

dphansti/Sushi documentation built on Oct. 30, 2021, 10:20 p.m.