kpPlotDensity: kpPlotDensity

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Plots the density of features along the genome

Usage

kpPlotDensity(karyoplot, data=NULL, window.size=1e6, 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 from which the density will be computed.
window.size	(numeric) The size of the windows for wich the density is computed. (Defaults to 1e6, one megabase windows)
ymin	(numeric) The minimum value to be plotted on the data panel. If NULL, it is set to 0. (deafults to NULL)
ymax	(numeric) The maximum value to be plotted on the data.panel. If NULL the maximum density is used. (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. In particular col and border can be used to set the colors used.

Details

kpPlotDensity plots the density of a set of features represented by a GRanges object along the genome. It creates a non-overlapping tiling of the genome and computes the number of features per window. It's possible to specify the window size.

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

Value

Returns the original karyoplot object with the data computed (windows and density) stored at karyoplot$latest.plot

See Also

plotKaryotype, kpPlotRibbon, kpPlotCoverage

Examples

set.seed(1000)

data <- createRandomRegions(nregions=20000)
 
kp <- plotKaryotype("hg19", plot.type=2, chromosomes="chr1")

kp <- kpPlotDensity(kp, data)
kpAxis(kp, ymin = 0, ymax=kp$latest.plot$computed.values$max.density)

kp <- kpPlotDensity(kp, data, data.panel=2, col="#CCCCFF",  ymax=20, lwd=2)
kpAxis(kp, ymin = 0, ymax=20, data.panel=2)

kp <- kpLines(kp, data=kp$latest.plot$computed.values$windows, y=kp$latest.plot$computed.values$density, col="black", r0=0.5, r1=1, data.panel=2, ymax=20)

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