kpAddLabels: kpAddLabels

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

kpAddLabels

Description

Add labels to identify the data in the plot

Usage

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

Arguments

karyoplot	a karyoplot object returned by a call to plotKaryotype
labels	(character) the text on the labels
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)
side	("left" or "right") The side of the plot where to plot the labels. (defaults to "left")
pos	(numeric) The standard graphical parameter. See text. If NULL, pos will be selected automatically based on "side" (Defaults to NULL)
offset	(numeric) The standard graphical parameter. See text. (Defaults to 0)
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)
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)
...	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

plot.params <- getDefaultPlotParams(plot.type=2)
plot.params$leftmargin <- 0.2
plot.params$rightmargin <- 0.2

#In standard whole karyotypes, labels are drawn for all chromosomes

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 = 0.12, 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)

#Plot on the right
#data panel 1
kpAddLabels(kp, "Everything", label.margin = 0.12, srt=90, pos=1, cex=0.8, side="right")
kpAddLabels(kp, "Red", r0=0, r1=0.5, cex=0.6, side="right")
kpAddLabels(kp, "Green", r0=0.5, r1=1, cex=0.6, side="right")
 
 
 
#In karyotypes with all chromosomes in a single line, 
#labels are added on the first (side="left") or last (side="right") chromosome

kp <- plotKaryotype("hg19", chromosomes=c("chr1", "chr2", "chr3"), plot.type=3, 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 = 0.12, 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)

#Plot on the right
#data panel 1
kpAddLabels(kp, "Everything", label.margin = 0.12, srt=90, pos=1, cex=0.8, side="right")
kpAddLabels(kp, "Red", r0=0, r1=0.5, cex=0.6, side="right")
kpAddLabels(kp, "Green", r0=0.5, r1=1, cex=0.6, side="right")



#In Zoomed regions, they are placed at the correct position too
kp <- plotKaryotype("hg19", zoom="chr1:20000000-40000000", plot.type=2, plot.params = plot.params)
kpAddBaseNumbers(kp, tick.dist=5000000, add.units=TRUE)
#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 = 0.12, 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)

#Plot on the right
#data panel 1
kpAddLabels(kp, "Everything", label.margin = 0.12, srt=90, pos=1, cex=0.8, side="right")
kpAddLabels(kp, "Red", r0=0, r1=0.5, cex=0.6, side="right")
kpAddLabels(kp, "Green", r0=0.5, r1=1, cex=0.6, side="right")

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