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 .
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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 1.38.0
Index]