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pvclust (version 1.2-2)

plot.pvclust: 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.

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.

See Also

text.pvclust