plotPairs: Plot tree-pairs
In HELP: Tools for HELP data analysis

Description Usage Arguments Author(s) See Also Examples

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

1	plotPairs(x, ...)

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.

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

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

#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)