Axis

Adding Y axis to our plots may help interpreting the magnitudes of plotted data and identifying the space dedicated to each plot. To do that we can use the kpAxis function.

kp <- plotKaryotype(plot.type=2, chromosomes=c("chr1", "chr2"))
kpDataBackground(kp)
kpDataBackground(kp, data.panel = 2)
kpAxis(kp, data.panel=1)
kpAxis(kp, data.panel=2)

Axis can be plotted at either left or right side of any on the data plots using the side parameter: 1 for left, 2 for right.

kp <- plotKaryotype(plot.type=2, chromosomes=c("chr1", "chr2"))
kpDataBackground(kp)
kpDataBackground(kp, data.panel = 2)
kpAxis(kp, data.panel=1, side = 2)
kpAxis(kp, data.panel=2)

And they can be customized in many ways:

• number of ticks and their positions and labels (with numticks, tick.pos and labels)
• colors of the lines and text (with col)
• length of ticks (with tick.len Attention! the length is in number of bases!)
• on which chromosomes the axis has to be drawn (with chromosomes (can be first, last, all or a vector of chromosome names)). By default in plot types 1, 2 and 6 (vertically stacked chromosomes) the axis will be plotted in all chromosomes and in plot types 3, 4, 5 and 7 (all chromosomes in a single line) only in the first (or last if side=2) chromosome
• all standard graphical parameters

kp <- plotKaryotype(plot.type=2, chromosomes=c("chr1", "chr2", "chr3", "chr4"))
kpDataBackground(kp)
kpDataBackground(kp, data.panel = 2)
kpAxis(kp, data.panel=1, side = 1, numticks = 4, tick.pos = c(0, 0.6, 0.8, 1), labels = c("none", 0.6, 0.8, "all") )
kpAxis(kp, data.panel=1, side = 2, col="red", chromosomes = c("chr1", "chr3"))
kpAxis(kp, data.panel=2, tick.len = 20e6, srt=45, lwd=3, lty=4)

Finally, the vertical positioning of the axis can be controlled with r0 and r1 as with most plotting functions. With this, we can use axis to mark different track like regions in the data panels. In addition, ymin and ymax can be used to set the extrem values for the axis.

kp <- plotKaryotype(plot.type=4, chromosomes=c("chr1", "chr2"))
kpDataBackground(kp, r0=0, r1=0.33, color = "cornflowerblue")
kpAxis(kp, numticks = 6, r0=0, r1=0.33, ymin=0, ymax=5 )
kpDataBackground(kp, r0=0.35, r1=0.8, color = "darkolivegreen1")
kpAxis(kp, numticks = 5, r0=0.35, r1=0.8, ymin=0, ymax=1 )
kpDataBackground(kp, r0=0.82, r1=1, color = "cadetblue2")
kpAxis(kp,  numticks = 3, r0=0.82, r1=1, ymin=-1, ymax=1 )