kpAddLabels {karyoploteR} | R Documentation

## 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")

[Package karyoploteR version 1.20.3 Index]