kpAddLabels: kpAddLabels

Description Usage Arguments Details Value See Also Examples

View source: R/kpAddLabels.R

Description

Add labels to identify the data in the plot

Usage

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kpAddLabels(karyoplot, labels, r0=NULL, r1=NULL, label.margin=0.01, data.panel=1, pos=2, offset=0, ...)

Arguments

karyoplot

a karyoplot object returned by a call to plotKaryotype

labels

(character) the text on the labels

r0

(numeric) r0 and r1 define the vertical range of the data panel to be used to position the label. 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 position the label. 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)

label.margin

(numeric) the additional the margin between the labels the first base of the chromosome. In plot coordinates. Usual value might be 0.05. Can be negative. (defaults to 0.01)

data.panel

(numeric) The identifier of the data panel where the labels are to be added. The available data panels depend on the plot type selected in the call to plotKaryotype. (defaults to 1)

pos

(numeric) The standard graphical parameter. See text. (Defaults to 2)

offset

(numeric) The standard graphical parameter. See text. (Defaults to 0)

...

any additional parameter to be passed to the text plotting. All R base graphics params are passed along.

Details

Given a KaryoPlot object, plot labels on the side of the data panels to help identify the different types of data plotted

Value

invisibly returns the given karyoplot object

See Also

plotKaryotype

Examples

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plot.params <- getDefaultPlotParams(plot.type=2)
plot.params$leftmargin=0.2
kp <- plotKaryotype("hg19", chromosomes=c("chr1", "chr2"), plot.type=2, plot.params = plot.params)
#data panel 1
kpDataBackground(kp, r0=0, r1=0.5, col="#FFDDDD")
kpDataBackground(kp, r0=0.5, r1=1, col="#DDFFDD")
kpAddLabels(kp, "Everything", label.margin = 0.1, srt=90, pos=3, cex=0.8)
kpAddLabels(kp, "Red", r0=0, r1=0.5, cex=0.6)
kpAddLabels(kp, "Green", r0=0.5, r1=1, cex=0.6)
#data panel 2
kpDataBackground(kp, col="#DDDDFF", data.panel = 2)
kpAddLabels(kp, "BLUE", data.panel=2)
 

Bioconductor-mirror/karyoploteR documentation built on July 4, 2017, 6:39 p.m.