plotScaleSpace {KCsmart} | R Documentation

## Plot multiple significant regions in one figure

### Description

Plots significant regions in different scale spaces in one figure

### Usage

    plotScaleSpace(spms, sigLevels, chromosomes=NULL, type='b')

### Arguments

`spms` | List of sample point matrices
`sigLevels` | List of significance levels
`chromosomes` | Takes a vector of chromosomes to be plotted. Defaults to all chromosomes.
`type` | Determines which data is plotted. 'g' for gains only, 'l' for losses only and 'b' for both. When type='b' is used, two devices (x11) will be opened.

### Details

Takes sample point matrices that were calculated using (different) kernel widths (sigma), then calculates the significant regions given the cutoffs as defined by 'sigLevels' and plots these in one figure.

### Value

Depending on the 'type' parameter, produces one or two plots, one for the gains and one for the losses. The heatmap color indicates the level of the gain or loss.

### Author(s)

Jorma de Ronde

### See Also

`plot`

### Examples

    data(hsSampleData)
    data(hsMirrorLocs)

    spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)
    spm4mb <- calcSpm(hsSampleData, hsMirrorLocs, sigma=4000000)

    siglevel1mb <- findSigLevelTrad(hsSampleData, spm1mb, n=3)
    siglevel4mb <- findSigLevelTrad(hsSampleData, spm4mb, n=3)

    plotScaleSpace(list(spm1mb, spm4mb), list(siglevel1mb, siglevel4mb), type='g')

[Package KCsmart version 1.6.0 Index]