kpAddBaseNumbers: kpAddBaseNumbers

Description Usage Arguments Details Value See Also Examples

View source: R/kpAddBaseNumbers.R

Description

Plots the base numbers along the chromosome ideograms

Usage

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kpAddBaseNumbers(karyoplot, tick.dist=20000000, tick.len=5, minor.ticks=TRUE, minor.tick.dist=5000000, minor.tick.len=2,  cex=0.5, tick.col=NULL, minor.tick.col=NULL, ...)

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

tick.len

(numeric) The length of the major tick marks in plot coordinates

minor.ticks

(boolean) Whether to add unlabeled minor ticks between the major ticks

minor.tick.dist

(numeric) The distance between the minor ticks in bases

minor.tick.len

(numeric) The length of the minor tick marks in plot coordinates

cex

(numeric) The cex parameter for the major ticks label

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)

...

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 witll 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

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kp <- plotKaryotype()
kpAddBaseNumbers(kp)

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


 

Bioconductor-mirror/karyoploteR documentation built on July 4, 2017, 6:39 p.m.