plotCMDS {yarn} | R Documentation

## Plot classical MDS of dataset

### Description

This function plots the MDS coordinates for the "n" features of interest. Potentially uncovering batch effects or feature relationships.

### Usage

    plotCMDS(obj, comp = 1:2, normalized = FALSE, distFun = dist,
      distMethod = "euclidian", n = NULL, samples = TRUE, log = TRUE,
      plotFlag = TRUE, ...)

### Arguments

`obj` | ExpressionSet object or objrix.
`comp` | Which components to display.
`normalized` | TRUE / FALSE, use the normalized matrix or raw counts.
`distFun` | Distance function, default is dist.
`distMethod` | The distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given.
`n` | Number of features to make use of in calculating your distances.
`samples` | Perform on samples or genes.
`log` | TRUE/FALSE log2-transform raw counts.
`plotFlag` | TRUE/FALSE whether to plot or not.
`...` | Additional plot arguments.

### Value

coordinates

### Examples

    data(skin)
    res <- plotCMDS(skin,pch=21,bg=factor(pData(skin)$SMTSD))

    # library(calibrate)
    # textxy(X=res[,1],Y=res[,2],labs=rownames(res))

[Package yarn version 1.14.0 Index]