pvclust: pvpick – R documentation

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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=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 suzuki@ef-prime.com

pvclust

Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling

v2.2-0

GPL (>= 2)

Authors

Ryota Suzuki <suzuki@ef-prime.com>, Yoshikazu Terada <terada@sigmath.es.osaka-u.ac.jp>, Hidetoshi Shimodaira <shimo@i.kyoto-u.ac.jp>

Initial release

2019-11-19