plotGenome {CNAnorm} | R Documentation

## Methods for Function plotGenome in Package ‘CNAnorm’

### 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 s.berri@leeds.ac.uk and Arief Gusnanto a.gusnanto@leeds.ac.uk

### 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')

[Package CNAnorm version 1.36.0 Index]