plotCopyNumberCallsAsLines: plotCopyNumberCallsAsLines

In bernatgel/CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

plotCopyNumberCallsAsLines

Description

Plot the segments representing the copy number calls by any algorithm

Usage

plotCopyNumberCallsAsLines(karyoplot, cn.calls, style="line", cn.column="cn", labels=NULL, label.cex=1, add.axis=TRUE, axis.cex=1, numticks=NULL, col="black", ymin=NULL, ymax=NULL, r0=0, r1=1, ...)

Arguments

karyoplot	(a KaryoPlot object) The object returned by the plotKaryotype function and representing the current active plot.
cn.calls	(a GRanges, a list of GRanges or a GRangesList) An object with the positions of the CN calls and a column with the CN values. Other columns are ignored. If it's a list of GRanges with different samples, all samples will be plotted, splitting the total plot space between them.
style	(character) The style in which the lines can be plot. It colud be as lines or segments. (defaults to "line")
cn.column	(integer or character vector) The name or number of the column with CN information.(defaults to "cn")
labels	(character) The text of the label to identify the data. If NA, no label will be plotted. If NULL, if snps is a single sample GRanges it will default to "Segments", if it's a list of samples it will default to the names in the list or consecutive numbers if names(snps) is NULL. (defaults to NULL)
label.cex	(numeric) The size of the label (defaults to 1)
add.axis	(logical) Whether to plot an axis (defaults to TRUE)
axis.cex	(numeric) The size of the axis labels.(defaults to 1)
numticks	The number of tocks in the axis (defaults to NULL)
col	(color) The color of the lines (defaults to "black")
ymin	(numeric) (karyoploteR parameter) The minimum value of y to be plotted. If NULL, it is set to the min value of the selected data panel. (defaults to -4)
ymax	(numeric) (karyoploteR parameter) (numeric) The maximum value of y to be plotted. If NULL, it is set to the max value of the selected data panel. (defaults to 2)
r0	(numeric) (karyoploteR parameter) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to 0)
r1	(numeric) (karyoploteR parameter) r0 and r1 define the vertical range of the data panel to be used to draw this plot. They can be used to split the data panel in different vertical ranges (similar to tracks in a genome browser) to plot differents data. If NULL, they are set to the min and max of the data panel, it is, to use all the available space. (defaults to 1)
...	The ellipsis operator can be used to specify any additional graphical parameters. Any additional parameter will be passed to the internal calls to karyoploteR functions.

Details

Plots the segments

Value

Invisibly returns the karyoplot object representing the plot. With it it is possible to add other elements to the plot using standrad karyoploteR functions

Examples

cncalls.file <- system.file("extdata", "S1.segments.txt", package = "CopyNumberPlots", mustWork = TRUE)
cncalls <- loadCopyNumberCalls(cncalls.file)

kp <- plotKaryotype("hg19")
#plotCopyNumberCallsAsLines(kp, cncalls)

kp <- plotKaryotype("hg19", chromosomes="chr3")
#plotCopyNumberCalls(kp, cncalls, r0=0, r1=0.2)
#plotCopyNumberCallsAsLines(kp, cncalls, r0=0.25, r1=0.55)
#plotCopyNumberCallsAsLines(kp, cncalls, r0=0.65, r1=0.95, style="segments", col="red", ymin=0, ymax=4, numticks=3)

kp <- plotKaryotype("hg19")
#plotCopyNumberCallsAsLines(kp, cncalls, r0=0.2, r1=0.4, style="segments", add.axis=FALSE, labels="CopyNumber")

#List of GRanges
cncalls.list <- list(s1=cncalls, s2 =cncalls)
kp <- plotKaryotype("hg19")
#plotCopyNumberCallsAsLines(kp, cncalls.list,style="segments", add.axis=FALSE)

bernatgel/CopyNumberPlots documentation built on Sept. 22, 2023, 1:53 a.m.