HELP (version 1.30.0)

plotPairs: 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.

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)