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Last data update: 2014.03.03

R: adds a legend to a Sushi plot

addlegend

R Documentation

adds a legend to a Sushi plot

Description

This function adds a legend to Sushi plots that have a colorby function (e.g. plotHic, plotGenes, and plotBedpe)

Usage

addlegend(range, title = "", labels.digits = 1, palette = topo.colors,
  side = "right", labelside = "left", xoffset = 0.1, width = 0.05,
  bottominset = 0.025, topinset = 0.025, tick.num = 5,
  tick.length = 0.01, txt.font = 1, txt.cex = 0.75, title.offset = 0.05,
  title.font = 2, title.cex = 1)

Arguments

`range`	the rang of values to be plotted. ie c(min,max)
`title`	title of values to be mapped
`labels.digits`	Number of digits after the decimal point to include in labels
`palette`	color palette to use
`side`	side of plot to place legend ('right','left')
`labelside`	side of legend to place legend title
`xoffset`	fraction of plot to offset the legend
`width`	width as a fraction of the plot width
`bottominset`	inset from the bottom of the blot as a fraction of the plot width
`topinset`	inset from the top of the blot as a fraction of the plot width
`tick.num`	desired number of tickmarks
`tick.length`	length of tick marks
`txt.font`	font type of legend text
`txt.cex`	font size of legned text
`title.offset`	offset of title from the key
`title.font`	font type of legend title
`title.cex`	font size of legned text

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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Type 'license()' or 'licence()' for distribution details.

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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/addlegend.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addlegend
> ### Title: adds a legend to a Sushi plot
> ### Aliases: addlegend
> 
> ### ** 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 
>