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.
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=NULL, ...)
# S3 method for pvclust
lines(x, alpha=0.95, pv="au", type="geq", col=2, lwd=2, ...)
object of class pvclust.
threshold value for \(p\)-values.
character string which specifies the \(p\)-value to be
used. It should be one of "si", "au" and "bp",
corresponding to SI, AU \(p\)-value and BP value, respectively. See
plot.pvclust for details.
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 displayed. Likewise "leq"
stands for lower than or equals, "gt" for
greater than and "lt" for lower than the
threshold value. The default is "geq".
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.
numeric value which specifies the color of borders of rectangles.
numeric value which specifies the color of lines.
numeric value which specifies the width of lines.
other graphic parameters to be used.
pvpick returns a list which contains the following values.
a list of character string vectors. Each vector corresponds to the names of objects in each cluster.
numeric vector of edge numbers. The \(i\)'th element
(number) corresponds to the \(i\)'th name vector in
clusters.