pvpick: Find Clusters with High/Low P-values

Description

find clusters with relatively high/low $p$-values. pvrect and lines (S3 method for class pvclust) highlight such clusters in existing plot, and pvpick returns a list of such clusters.

Usage

pvpick(x, alpha=0.95, pv="au", type="geq", max.only=TRUE)
pvrect(x, alpha=0.95, pv="au", type="geq", max.only=TRUE, border=2, ...)
## S3 method for class 'pvclust':
lines(x, alpha=0.95, pv="au", type="geq", col=2, lwd=2, ...)

Arguments

object of class pvclust.

alpha

threshold value for $p$-values.

character string which specifies the $p$-value to be used. It should be either of "au" or "bp", corresponding to AU $p$-value or BP value, respectively. See plot.pvclust for details.

type

one of "geq", "leq", "gt" or "lt". If "geq" is specified, clusters with $p$-value greater than or equals the threshold given by "alpha" are returned or disp

max.only

logical. If some of clusters with high/low $p$-values have inclusion relation, only the largest cluster is returned (or displayed) when max.only=TRUE.

border

numeric value which specifies the color of borders of rectangles.

col

numeric value which specifies the color of lines.

lwd

numeric value which specifies the width of lines.

...

other graphic parameters to be used.

Value

pvpick returns a list which contains the following values.
clustersa list of character string vectors. Each vector corresponds to the names of objects in each cluster.
edgesnumeric vector of edge numbers. The $i$'th element (number) corresponds to the $i$'th name vector in clusters.