pvpick: Find Clusters with High/Low P-values

In pvclust: Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling

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=NULL, ...)

## S3 method for class 'pvclust'
lines(x, alpha=0.95, pv="au", type="geq", col=2, lwd=2, ...)

Arguments

x	object of class pvclust.
alpha	threshold value for p-values.
pv	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.
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 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".
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.

clusters	a list of character string vectors. Each vector corresponds to the names of objects in each cluster.
edges	numeric vector of edge numbers. The i'th element (number) corresponds to the i'th name vector in clusters.

Author(s)

Ryota Suzuki [e-mail]

pvclust documentation built on Nov. 19, 2019, 5:07 p.m.