plotGenome-methods: Methods for Function plotGenome in Package 'CNAnorm'

In CNAnorm: A normalization method for Copy Number Aberration in cancer samples

Description

plotGenome plot normalized ratio and optionally segmented and/or smoothed normalized ratio values in Package ‘CNAnorm’. It also shows annotation.

Usage

## S4 method for signature 'CNAnorm'
plotGenome(object, maxRatio = 8, minRatio = -1,
    superimpose = character(0),  gPar = NULL, numHorLables = 10, 
    colorful = FALSE,  show.centromeres = TRUE, idiogram = NULL, fixVAxes = FALSE, 
    supLineColor = character(0), supLineCex = character(0), dot.cex = .2, ...)

Arguments

object	An object of Class "CNAnorm"
maxRatio	The maximum ratio to be shown on the plot. Values or ratio greater than maxRatio will be displayed as green triangulars
minRatio	The minimum ratio to be shown on the plot. Values or ratio smaller than minRatio will be displayed as green triangulars
superimpose	A character verctor with one or both of the following: "smooth", "DNACopy"
numHorLables	. Number of maximum horizontal lables. The function will try to annotate numHorLables so that they are approximately equally spaced.
colorful	A switch to decide if the background dots representing the ratio of each window should be gray or colored according their value in relation to the peak closest to the median
show.centromeres	A switch to decide if location of centromere are displayed on the graph. The location of the centromere is stored in idiogram
idiogram	A data frame containing banding information. if NULL -default- human information will be loaded by data(hg19_hs_ideogr)
fixVAxes	A switch to decide if the vertical axes should be fixed to minRatio and maxRatio or fit the data within minRatio and maxRatio.
gPar	a S3 object with all graphical parameters. If NULL (default) data(gPar) is called
supLineColor	A three element character vector with colors to be used for first superimposed line, second superimposed line, normalized ratio dots. If none is provided, defaults are: c("black", "cyan", "grey60")
supLineCex	A two element vector with cex valeus to be used for width of first superimposed line and second superimposed line. If none is provided, defaults are: c(0.5, 0.5)
dot.cex	size of the dots in the plot
...	Further arguments to pass to the function plot

Value

An object of class "CNAnorm"

Author(s)

Stefano Berri [e-mail] and Arief Gusnanto [e-mail]

See Also

plot, par, peakPloidy, gPar, hg19_hs_ideogr

Examples

data(CN)
# see peakPloidy documentation to know how object CN is created
CN <- addDNACopy(CN)
CN <- validation(CN)
CN <- discreteNorm(CN)
plotGenome(CN, superimpose = 'DNACopy')

CNAnorm documentation built on Nov. 8, 2020, 5:29 p.m.