kpAddBaseNumbers: kpAddBaseNumbers

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

kpAddBaseNumbers

Description

Plots the base numbers along the chromosome ideograms

Usage

kpAddBaseNumbers(karyoplot, tick.dist=20000000, tick.len=5, units="auto", add.units=FALSE, digits=2, minor.ticks=TRUE, minor.tick.dist=5000000, minor.tick.len=2,  cex=0.5, tick.col=NULL, minor.tick.col=NULL, clipping=TRUE, ...)

Arguments

karyoplot	(karyoplot object) A valid karyoplot object created by a call to plotKaryotype
tick.dist	(numeric) The distance between the major numbered tick marks in bases (defaults to 20 milions, one major tick every 20Mb)
tick.len	(numeric) The length of the major tick marks in plot coordinates (defaults to 5)
units	(character) the units for the numbers to be represented. Must be one of "auto", "b", "kb" or "Mb". If auto, it will utomatically choose the most suitable unit. (Defaults to "auto")
add.units	(boolean) Add the units (Mb, Kb...) to the tick labels. (Defaults to FALSE)
digits	(integer) The maximum number of digits after the decimal point in labels. (defaults to 2)
minor.ticks	(boolean) Whether to add unlabeled minor ticks between the major ticks (defaults to TRUE)
minor.tick.dist	(numeric) The distance between the minor ticks in bases (defaults to 5 milions, a minor tick mark every 5Mb)
minor.tick.len	(numeric) The length of the minor tick marks in plot coordinates (defaults to 2)
cex	(numeric) The cex parameter for the major ticks label (defaults to 0.5)
tick.col	(color) If specified, the color to plot the major ticks. Otherwise the default color or, if given, the col parameter will be used. (Defaults to NULL)
minor.tick.col	(color) If specified, the color to plot the minor ticks. Otherwise the default color or, if given, the col parameter will be used. (Defaults to NULL)
clipping	(boolean) Only used if zooming is active. If TRUE, the data representation will be not drawn out of the drawing area (i.e. in margins, etc) even if the data overflows the drawing area. If FALSE, the data representation 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 the base numbers scale to the chromosome ideograms. The base numbers and ticks will be drawn next to the ideograms and not on a separate independent x axis. It is possible to control the number and position of the tick marks and labels

Value

Returns the original karyoplot object, unchanged.

See Also

plotKaryotype

Examples

 

kp <- plotKaryotype()
kpAddBaseNumbers(kp)

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


 

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