R: Draws Dendrogram with P-values for Pvclust Object

plot.pvclust {pvclust}

R Documentation

Draws Dendrogram with P-values for Pvclust Object

Description

plot dendrogram for a pvclust object and add p-values for clusters.

Usage

## S3 method for class 'pvclust'
plot(x, print.pv=TRUE, print.num=TRUE, float=0.01,
     col.pv=c(2,3,8), cex.pv=0.8, font.pv=NULL, col=NULL, cex=NULL,
     font=NULL, lty=NULL, lwd=NULL, main=NULL, sub=NULL, xlab=NULL, ...)

## S3 method for class 'pvclust'
text(x, col=c(2,3,8), print.num=TRUE, float=0.01, cex=NULL, font=NULL, ...)

Arguments

`x`	object of class `pvclust`, which is generated by function `pvclust`. See `pvclust` for details.
`print.pv`	logical flag to specify whether print p-values above the edges (clusters).
`print.num`	logical flag to specify whether print edge numbers below clusters.
`float`	numeric value to adjust the height of p-values from edges.
`col.pv`	numeric vector of length three to specify the colors for p-values and edge numbers. From the beginning each value corresponds to the color of AU values, BP values and edge numbers, respectively.
`cex.pv`	numeric value which specifies the size of characters for p-values and edge numbers. See `cex` argument for `par`.
`font.pv`	numeric value which specifies the font of characters for p-values and edge numbers. See `font` argument for `par`.
`col, cex, font`	in `text` function, they correspond to `col.pv`, `cex.pv` and `font.pv` in `plot` function, respectively. In `plot` function they are used as generic graphic parameters.
`lty, lwd, main, sub, xlab, ...`	generic graphic parameters. See `par` for details.

Details

This function plots a dendrogram with p-values for given object of class pvclust. AU p-value (printed in red color in default) is the abbreviation of "approximately unbiased" p-value, which is calculated by multiscale bootstrap resampling. BP value (printed in green color in default) is "bootstrap probability" value, which is less accurate than AU value as p-value. One can consider that clusters (edges) with high AU values (e.g. 95%) are strongly supported by data.

Author(s)

Ryota Suzuki suzuki@ef-prime.com

References

Shimodaira, H. (2004) "Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling", Annals of Statistics, 32, 2616-2641.

Shimodaira, H. (2002) "An approximately unbiased test of phylogenetic tree selection", Systematic Biology, 51, 492-508.