kpAddCytobandsAsLine: kpAddCytobandsAsLine

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Plots the chromosome cytobands in a karyoplot as a line

Usage

kpAddCytobandsAsLine(karyoplot, color.table=NULL, color.schema='only.centromeres', lwd=3, lend=1, 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: 'only.centromeres', 'circos', 'biovizbase') The name of the color schema to use. It is directly passed along to getCytobandColors. color.table takes precendence over color.schema. (defaults to 'only.centromeres')
lwd	(integer) The width of the line used to represent the ideogram (defaults to 3)
lend	(0, 1 or 2) The type of line end. (defaults to 1, "butt")
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. In contrast to kpAddCytobands it represents the chromosomes as a thin line

Value

invisibly returns the given karyoplot object

Note

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

See Also

plotKaryotype, getCytobandColors, kpAddBaseNumbers, kpAddCytobandLabels

Examples

kp <- plotKaryotype(ideogram.plotter = NULL)
kpAddCytobandsAsLine(kp)
 
kp <- plotKaryotype(ideogram.plotter = NULL, plot.type=2)
kpAddCytobandsAsLine(kp)
 

karyoploteR documentation built on Nov. 8, 2020, 5:52 p.m.