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. cor.method the correlation algorithm to be used. This must be one of "pearson" (default), "kendall", or "spearman". Any unambiguous substring can be given: see `cor` for more details. \dots 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 1.48.0 Index]