kpPoints: kpPoints

In bernatgel/karyoploteR: Plot customizable linear genomes displaying arbitrary data

kpPoints

Description

Plots data points along the genome.

Usage

kpPoints(karyoplot, data=NULL, chr=NULL, x=NULL, y=NULL, ymin=NULL, ymax=NULL, data.panel=1, r0=NULL, r1=NULL, clipping=TRUE, pch=16, cex=0.5, ...)

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)
pch	(numeric) the glyph to represent the points as specified in par. (defaults to 16, a solid circle)
cex	(numeric) the relative size of the glyphs as defined at par. (defaults to 0.5)
...	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 the set of points representing 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 points are drawn. In addition, via the ellipsis operator (...), kpPoints accepts any parameter valid for points (e.g. pch, cex, col, ...)

There's more information at the https://bernatgel.github.io/karyoploter_tutorial/karyoploteR tutorial.

Value

Returns the original karyoplot object, unchanged.

Note

The parameter r0 can be used to specify r0 and r1 together. If r1 is NULL and r0 is either a list with two elements called r0 and r1 or a numeric vector of length 2, this values will be used for r0 and r1. This might be useful when working with autotrack to compute r0 and r1.

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, cex=0.5)
  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)
  #and we can specify r0 and r1 in r0
  kpPoints(kp, data=data.points, r0=list(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)  


 

bernatgel/karyoploteR documentation built on Feb. 1, 2024, 11:48 p.m.