kpAddCytobandLabels: kpAddCytobandLabels

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

kpAddCytobandLabels

Description

Plots the base numbers along the chromosome ideograms

Usage

kpAddCytobandLabels(karyoplot, cex=0.5, force.all=FALSE, clipping=TRUE, ...)

Arguments

karyoplot	(karyoplot object) A valid karyoplot object created by a call to plotKaryotype
cex	(numeric) The cex parameter for the cytoband labels
force.all	(boolean) If true, all cytoband labels are plotted, even if they do not fit into the cytobands (Defaults to FALSE)
clipping	(boolean) Only used if zooming is active. If TRUE, the name will be not drawn out of the drawing are (i.e. in margins, etc) even if the data overflows the drawing area. If FALSE, the labels may overflow into the margins of the plot. (defaults to TRUE)
...	Any other parameter to be passed to internal function calls. Specially useful for graphic parameters.

Details

This function can be used to add labels idenfifying the cytobands. It gets the labels from the cytobands information stored in the karyoplot object and it will only plot the labels that fit inside the available space. This means than in some cases (such as when plotting a complete genome with default parameters) it is possible that no labels at all are added.

Value

Returns the original karyoplot object, unchanged.

See Also

plotKaryotype

Examples

  
kp <- plotKaryotype()
kpAddBaseNumbers(kp)
kpAddCytobandLabels(kp)

kp <- plotKaryotype(chromosomes="chr17")
kpAddBaseNumbers(kp, tick.dist=10000000, minor.tick.dist=1000000)
kpAddCytobandLabels(kp)

 

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