Knowledge base

Sushi packge to plot Bedpe figure

Introduction

The BEDPE format can concisely describe disjoint genome features, such as structural variations or paired end sequence alignments. The plotBedpe function can visualize it.

Code explanation

Input

bedpe format data frame。

head(Sushi_5C.bedpe)

As follows

    chrom1 start1 end1 chrom2 start2 end2 name score strand1
chr2 234208447 234223064 chr2 234156762 234159135 NA 44.39862 .
chr15 41711734 41718116 chr15 41802421 41808201 NA 20.62534 .
chr11 64172456 64183193 chr11 64068878 64079209 NA 16.91630 .
chr2 234208447 234223064 chr2 234163674 234170252 NA 12.34501 .
chr6 41755186 41769245 chr6 41435903 41452283 NA 11.63480 .
chr11 64159283 64172456 chr11 64068878 64079209 NA 11.13098 .
strand2 samplenumber
. 1
. 1
. 1
. 1
. 1
. 1
Code example
library('Sushi')  # 加载Sushi包

Sushi_data = data(package ='Sushi') # 列出Sushi自带的数据
data(list = Sushi_data$results[,3]) # 载入data

chrom = "chr11"
chromstart = 1650000
chromend = 2350000

pbpe = plotBedpe(Sushi_5C.bedpe,chrom,chromstart,chromend,
heights = Sushi_5C.bedpe$score,plottype="loops",
colorby=Sushi_5C.bedpe$samplenumber,colorbycol=SushiColors(3))

labelgenome(chrom, chromstart,chromend,n=3,scale="Mb") # Add coordinate

legend("topright",inset =0.01,legend=c("K562","HeLa","GM12878"),col=SushiColors(3)(3),pch=19,bty='n',text.font=2)  # Add legend

axis(side=2,las=2,tcl=.2)  # Add y axis

mtext("Z-score",side=2,line=1.75,cex=.75,font=2) # y text

It can also be displayed like the UCSC transcriptome, using flip=TRUE to set the axis on the top, and plottype="lines" to display in the form of lines.

chrom = "chr11"
chromstart = 1650000
chromend = 2350000

pbpe = plotBedpe(Sushi_5C.bedpe,chrom,chromstart,chromend,flip=TRUE,
plottype="lines",colorby=Sushi_5C.bedpe$score,colorbycol=SushiColors(5))

labelgenome(chrom, chromstart,chromend,side=3,n=3,scale="Mb") 

addlegend(pbpe[[1]],palette=pbpe[[2]],title="Z-score",side="right",bottominset=0.05,
topinset=0.05,xoffset=-.035,labelside="right",width=0.025,title.offset=0.045)

Reference

https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

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