Bclabels: Plot bootstrap values

In shipunov: Miscellaneous Functions from Alexey Shipunov

Plot bootstrap values

Description

Print (bootstrap) values on 'hclust' plot

Usage

Bclabels(hcl, values, coords=NULL, horiz=FALSE, method="text",
 threshold=NULL, top=NULL, percent=FALSE, ...)

Arguments

hcl	hclust object
values	numeric, (bootstrap) values to use
coords	If NULL (default), coordinates will be calculated with Hcoords(hcl)
horiz	Plot values for a horizontal tree?
method	If "text" (default), plot text values, if "points", plot points
threshold	If set, do not plot text or points for values < threshold; respects percents if set
top	If set as 'n', plot values only for 'n' highest clusters
percent	Plot values as percents?
...	If "text" (default), additional arguments to text(), if "points", to points()

Details

This low-level plot function plots text or points in accordance with bootstrap values to the corresponding node of the plotted 'hclust' object.

Value

List with components: 'coords' for coordinates, 'labels' for (selected) values.

See Also

Bclust

Examples

## 'atmospheres' data
(bb <- Bclust(t(atmospheres))) # specify 'mc.cores=4' or similar to speed up the process

## standard use
plot(bb$hclust)
Bclabels(bb$hclust, bb$values, col="blue", pos=3, offset=0.1, threshold=0.9)

## 'points' method
plot(bb$hclust)
Bclabels(bb$hclust, bb$values, method="points", threshold=0.9, pch=19, cex=2)

## 'points' which grow with support
plot(bb$hclust)
Bclabels(bb$hclust, bb$values, method="points", pch=19, cex=bb$values*3)

## pre-defined coordinates
coords1 <- Hcoords(bb$hclust)
plot(bb$hclust)
Bclabels(bb$hclust, bb$values, coords=coords1, method="points", pch=19,
 cex=bb$values*3)

## use with horizontal Ploth()
oldpar <- par(mar=c(2,1,0,4))
Ploth(bb$hclust, horiz=TRUE)
Bclabels(bb$hclust, bb$values, col="blue", pos=3, offset=0.1, horiz=TRUE)
par(oldpar)

## 'moldino' data
m.bb <- Bclust(t(moldino)) # specify 'mc.cores=4' or similar to speed up the process
plot(m.bb$hclust)
Bclabels(m.bb$hclust, m.bb$values, col="red", pos=3, offset=0.1, threshold=0.5)

## 'iris' data, with hyper-binding to make number of variables reliable
iris.bb <- Bclust(iris[, rep(1:4, 6)], iter=100) # remove iter=100 for better bootstrap
plot(iris.bb$hclust, labels=FALSE, main="", xlab="", sub="Bootstrap, 100 replicates")
## use 'percent' and 'top'
Bclabels(iris.bb$hclust, iris.bb$values, top=5, percent=TRUE, pos=3, offset=0.1)
Fence(iris.bb$hclust, iris$Species)
legend("topright", legend=levels(iris$Species), col=1:3, lwd=2.5, bty="n")

shipunov documentation built on Feb. 16, 2023, 9:05 p.m.