R: Draws Dendrogram with P-values for Pvclust Object
plot.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.
providing 
.