kpAddCytobands: kpAddCytobands

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

kpAddCytobands

Description

Plots the chromosome cytobands in a karyoplot

Usage

kpAddCytobands(karyoplot, color.table=NULL, color.schema=c("circos", "biovizbase", "only.centromeres"), clipping=TRUE, ...)

Arguments

karyoplot	a karyoplot object returned by a call to plotKaryotype
color.table	(named character vector) a table specifying the colors to plot the cytobands. If NULL, it gets the colors calling getCytobandColors. (defaults to NULL)
color.schema	(character) The name of the color schema to use: circos, biovizBase, only.centromeres (everything in gray, except for centromeres in red). (defaults to circos)
clipping	(boolean) Only used if zooming is active. If TRUE, cytoband representation 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 cytobands representation may overflow into the margins of the plot. (defaults to TRUE)
...	any additional parameter to be passed to the functions called from kpAddCytobands.

Details

Plots the cytobands representing the chromosome structure in a karyoplot. It extracts the cytobands from the karyoplot object it recieves as a parameter. It is possible to specify the colors used to plot the cytobands.

Value

invisibly returns the given karyoplot object

Note

In general, this function is automatically called by plotKaryotype and the user never nees to call it.

See Also

plotKaryotype, getCytobandColors, kpAddBaseNumbers, kpAddCytobandLabels

Examples

kp <- plotKaryotype(ideogram.plotter = NULL)
kpAddCytobands(kp)
 

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