mdsPlot {minfi} | R Documentation

## Multi-dimensional scaling plots giving an overview of similarities and differences between samples.

### Description

Multi-dimensional scaling (MDS) plots showing a 2-d projection of distances between samples.

### Usage

    mdsPlot(dat, numPositions = 1000, sampNames = NULL, sampGroups = NULL, xlim, ylim,
        pch = 1, pal = brewer.pal(8, "Dark2"), legendPos = "bottomleft",
        legendNCol, main = NULL)

### Arguments

`dat` | An `RGChannelSet`, a `MethylSet` or a `matrix`. We either use the `getBeta` function to get Beta values (for the first two) or we assume the matrix contains Beta values.
`numPositions` | Use the `numPositions` genomic positions with the most methylation variability when calculating distance between samples.
`sampNames` | Optional sample names. See details.
`sampGroups` | Optional sample group labels. See details.
`xlim` | x-axis limits.
`ylim` | y-axis limits.
`pch` | Point type. See `par` for details.
`pal` | Color palette.
`legendPos` | The legend position. See `legend` for details.
`legendNCol` | The number of columns in the legend. See `legend` for details.
`main` | Plot title.

### Details

Euclidean distance is calculated between samples using the `numPositions` most variable CpG positions. These distances are then projected into a 2-d plane using classical multidimensional scaling transformation.

### Value

No return value. Plots are produced as a side-effect.

### Author(s)

Martin Aryee aryee@jhu.edu.

### References

I Borg, P Groenen. Modern Multidimensional Scaling: theory and applications (2nd ed.) New York: Springer-Verlag (2005) pp. 207-212. ISBN 0387948457.

http://en.wikipedia.org/wiki/Multidimensional_scaling

### See Also

`qcReport`, `controlStripPlot`, `densityPlot`, `densityBeanPlot`, `par`, `legend`

### Examples

    if (require(minfiData)) {

    names <- pData(MsetEx)$Sample_Name
    groups <- pData(MsetEx)$Sample_Group
    mdsPlot(MsetEx, sampNames=names, sampGroups=groups)

    }

[Package minfi version 1.28.4 Index]