plotBedpe: plots data stored in bed file format

In Sushi: Tools for visualizing genomics data

Description

plots data stored in bed file format

Usage

plotBedpe(bedpedata, chrom, chromstart, chromend, heights, color = "black",
  colorby = NULL, colorbycol = NULL, colorbyrange = NULL, border = NULL,
  lwdby = NULL, lwdrange = c(1, 5), offset = 0, flip = FALSE, lwd = 1,
  xaxt = "n", yaxt = "n", bty = "n", plottype = "loops",
  maxrows = 10000, height = 0.3, ymax = 1.04, ...)

Arguments

bedpedata	bed paired end data to be plotted
chrom	chromosome of region to be plotted
chromstart	start position
chromend	end position
heights	single value or vector specifying the height of the arches to be plotted (only valid when plottype is set to "loops" )
color	single value or vector specifying colors of bedpe elements
colorby	vector to scale colors by
colorbycol	palette to apply color scale to (only valid when colorby is not NULL)
colorbyrange	the range of values to apply the color scale to. Values outside that range will be set to the limits of the range.
lwdby	vector to scale line widths by
lwdrange	the range of values to apply the line width scale to. Values outside that range will be set to the limits of the range.
offset	offset of bedpe elements from the x-axis
flip	TRUE/FALSE whether the plot should be flipped over the x-axis
lwd	linewidth for bedpe elements (only valid when colorby is not NULL)
xaxt	A character which specifies the x axis type. See par
yaxt	A character which specifies the y axis type. See par
bty	A character string which determined the type of box which is drawn about plots. See par
plottype	type of plot (acceptable values are 'loops', 'ribbons', or 'lines')
maxrows	The maximum number of rows to plot on the y-axis
height	the height of the boxes at either end of a bedpe element if plottype is set to 'lines'. Typical vaues range form 0 to 1. (only valid when plottype is set to 'lines')
ymax	fraction of max y value to set as height of plot. Only applies when plottype is set to 'loops' or 'ribbons'
...	values to be passed to plot

Examples

data(Sushi_5C.bedpe)

chrom            = "chr11"
chromstart       = 1650000
chromend         = 2350000
pbpe = plotBedpe(Sushi_5C.bedpe,chrom,chromstart,chromend,heights = Sushi_5C.bedpe$score,offset=0,flip=FALSE,bty='n',
lwd=1,plottype="ribbons",colorby=Sushi_5C.bedpe$samplenumber,colorbycol=topo.colors,border="black")
labelgenome(chrom, chromstart,chromend,side=1,scipen=20,n=3,scale="Mb",line=.18,chromline=.5,scaleline=0.5)
legend("topright",inset =0.01,legend=c("K562","HeLa","GM12878"),col=c(topo.colors(3)),pch=19,bty='n',text.font=2)
axis(side=2,las=2,tcl=.2)
mtext("Z-score",side=2,line=1.75,cex=.75,font=2)

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
[1] 0.01467833
[1] 0.1027483
[1] ""
[1] 0.04582833
[1] 0.3207983
[1] ""
[1] 0.01322167
[1] 0.09255167
[1] ""
[1] 0.00528
[1] 0.03696
[1] ""
[1] 0.009596667
[1] 0.06717667
[1] ""
[1] 0.005646667
[1] 0.03952667
[1] ""
[1] 0.01035167
[1] 0.07246167
[1] ""
[1] 0.011745
[1] 0.082215
[1] ""
[1] 0.03432
[1] 0.24024
[1] ""
[1] 0.004385
[1] 0.030695
[1] ""
[1] 0.013995
[1] 0.097965
[1] ""
[1] 0.003825
[1] 0.026775
[1] ""
[1] 0.017155
[1] 0.120085
[1] ""
[1] 0.008725
[1] 0.061075
[1] ""
[1] 0.01321667
[1] 0.09251667
[1] ""
[1] 0.005021667
[1] 0.03515167
[1] ""
[1] 0.005393333
[1] 0.03775333
[1] ""
[1] 0.01155
[1] 0.08085
[1] ""
[1] 0.0005683333
[1] 0.003978333
[1] ""
[1] 0.03711333
[1] 0.2597933
[1] ""
[1] 0.006903333
[1] 0.04832333
[1] ""
[1] 0.01066833
[1] 0.07467833
[1] ""
[1] 0.01247333
[1] 0.08731333
[1] ""
[1] 0.02924167
[1] 0.2046917
[1] ""
[1] 0.03377333
[1] 0.2364133
[1] ""
[1] 0.03973
[1] 0.27811
[1] ""
[1] 0.016045
[1] 0.112315
[1] ""
[1] 0.01473
[1] 0.10311
[1] ""
[1] 0.01093
[1] 0.07651
[1] ""
[1] 0.02046
[1] 0.14322
[1] ""
[1] 0.006243333
[1] 0.04370333
[1] ""
[1] 0.01066833
[1] 0.07467833
[1] ""
[1] 0.011745
[1] 0.082215
[1] ""
[1] 0.004385
[1] 0.030695
[1] ""
[1] 0.01164667
[1] 0.08152667
[1] ""
[1] 0.01054167
[1] 0.07379167
[1] ""
[1] 0.01093
[1] 0.07651
[1] ""
[1] 0.009976667
[1] 0.06983667
[1] ""
[1] 0.01279667
[1] 0.08957667
[1] ""
[1] 0.01155
[1] 0.08085
[1] ""
[1] 0.04582833
[1] 0.3207983
[1] ""
[1] 0.005021667
[1] 0.03515167
[1] ""
[1] 0.001553333
[1] 0.01087333
[1] ""
[1] 0.004385
[1] 0.030695
[1] ""
[1] 0.01155
[1] 0.08085
[1] ""
[1] 0.009728333
[1] 0.06809833
[1] ""
[1] 0.01066833
[1] 0.07467833
[1] ""
[1] 0.011745
[1] 0.082215
[1] ""
[1] 0.04582833
[1] 0.3207983
[1] ""
[1] 0.04765
[1] 0.33355
[1] ""
[1] 0.03377333
[1] 0.2364133
[1] ""
There were 50 or more warnings (use warnings() to see the first 50)

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