kpLines: kpLines

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Plots a line joining the data points along the genome.

Usage

kpLines(karyoplot, data=NULL, chr=NULL, x=NULL, y=NULL, ymin=NULL, ymax=NULL, data.panel=1, r0=NULL, r1=NULL, clipping=TRUE, ...)

Arguments

karyoplot	(a KaryoPlot object) This is the first argument to all data plotting functions of karyoploteR. A KaryoPlot object referring to the currently active plot.
data	(a GRanges) A GRanges object with the data. If data is present, chr will be set to seqnames(data) and x to the midpoints of the rages in data. If no parameter y is specified and data has a column named y or value this column will be used to define the y value of each data point. (defaults to NULL)
chr	(a charecter vector) A vector of chromosome names specifying the chromosomes of the data points. If data is not NULL, chr is ignored. (defaults to NULL)
x	(a numeric vector) A numeric vector with the positions (in base pairs) of the data points in the chromosomes. If data is not NULL, x is ignored. (defaults to NULL)
y	(a numeric vector) A numeric vector with the values of the data points. If y is not NULL, it is used instead of any data column in data. (defaults to NULL)
ymin	(numeric) The minimum value of y to be plotted. If NULL, it is set to the min value of the selected data panel. (defaults to NULL)
ymax	(numeric) The maximum value of y to be plotted. If NULL, it is set to the max value of the selected data panel. (defaults to NULL)
data.panel	(numeric) The identifier of the data panel where the data is to be plotted. The available data panels depend on the plot type selected in the call to plotKaryotype. (defaults to 1)
r0	(numeric) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to NULL)
r1	(numeric) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to NULL)
clipping	(boolean) Only used if zooming is active. If TRUE, the data representation will be not drawn out of the drawing area (i.e. in margins, etc) even if the data overflows the drawing area. If FALSE, the data representation may overflow into the margins of the plot. (defaults to TRUE)
...	The ellipsis operator can be used to specify any additional graphical parameters. Any additional parameter will be passed to the internal calls to the R base plotting functions.

Details

This is one of the functions from karyoploteR implementing the adaptation to the genome context of basic plot functions from R base graphics. Given a set of positions on the genome (chromosome and base) and a value (y) for each of them, it plots a line joining them. Data can be provided via a GRanges object (data), independent parameters for chr, x and y or a combination of both. A number of parameters can be used to define exactly where and how the lines are drawn. In addition, via the ellipsis operator (...), kpLines accepts any parameter valid for lines (e.g. lwd, lty, col, ...) The lines are drawn in a per chromosome basis, so it is not possible to draw lines encompassing more than one chromosome.

Value

Returns the original karyoplot object, unchanged.

See Also

plotKaryotype, kpLines, kpText, kpPlotRegions

Examples

 
set.seed(1000)
data.points <- sort(createRandomRegions(nregions=500, mask=NA))
mcols(data.points) <- data.frame(y=runif(500, min=0, max=1))

kp <- plotKaryotype("hg19", plot.type=2, chromosomes=c("chr1", "chr2"))
  kpDataBackground(kp, data.panel=1)
  kpDataBackground(kp, data.panel=2)

  kpLines(kp, data=data.points, col="red")

  #Three ways of specifying the exact same data.points
  kpPoints(kp, data=data.points)
  kpPoints(kp, data=data.points, y=data.points$y, pch=16, col="#CCCCFF", cex=0.6)
  kpPoints(kp, chr=as.character(seqnames(data.points)), 
           x=(start(data.points)+end(data.points))/2, y=data.points$y, pch=".",
           col="black", cex=1)

  #plotting in the data.panel=2 and using r0 and r1, ymin and ymax
  kpLines(kp, data=data.points, col="red", r0=0, r1=0.3, data.panel=2)
  kpPoints(kp, data=data.points, r0=0, r1=0.3, data.panel=2, pch=".", cex=3)

  kpLines(kp, data=data.points, col="blue", r0=0.4, r1=0.7, data.panel=2)
  kpLines(kp, data=data.points, col="blue", y=-1*(data.points$y), 
          ymin=-1, ymax=0, r0=0.7, r1=1, data.panel=2)
  #It is also possible to "flip" the data by giving an r0 > r1
  kpPoints(kp, data=data.points, col="red", y=(data.points$y), 
           r0=1, r1=0.7, data.panel=2, pch=".", cex=2)  


 

karyoploteR documentation built on Nov. 8, 2020, 5:52 p.m.