plotPairs {HELP} | R Documentation

## Plot tree-pairs

### Description

Pairwise comparison of samples producing a matrix of scatterplots and a corresponding dendrogram

### Usage

    plotPairs(x, ...)

### Arguments

`x` | a numeric matrix, where each column represents a different sample. `x` can also be of class `"ExpressionSet"`.
`...` | Arguments to be passed to methods (see `plotPairs-methods`): `element` which element of `AssayData` to use for a given `ExpressionSet` input (default is "exprs") `samples` which samples to use as data. Can be a vector of characters matching sample names, integers indicating which samples to choose, or a mixture of the two. If NULL (default), all samples will be used. `scale` logical value indicating whether sample branch lengths should be scaled by distance (default is TRUE) `groups` logical value indicating whether the samples should be organized and color-coded by group (default is TRUE) `dist.method` the distance measure to be used. This must be one of "euclidean" (default), "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given: see `dist` for more details. `hclust.method` the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward" (default), "single", "complete", "average", "mcquitty", "median" or "centroid": see `hclust` for more details. `k` an integer scalar or vector with the desired number of groups. If NULL (default), grouping will rely instead on distance measurements: see `cutree` for more details. `...` other arguments to be passed to `pairs` or `dist`. See `pairs`, `dist`.

### Author(s)

Reid F. Thompson (rthompso@aecom.yu.edu)

### See Also

`plotPairs-methods`, `dist`, `hclust`, `dendrogram`, `cutree`, `pairs`

### Examples

    #demo(pipeline,package="HELP")

    x <- sample(1:10000,size=10000)
    x <- cbind(x,x+5,x*sample((1000:2000)/1000,size=10000,replace=TRUE),sample(-1*(1:10000),size=10000))
    colnames(x) <- c("x","x+5","spread","random")
    plotPairs(x)

    #rm(x)

[Package HELP version 1.0.0 Index]