DendSer (version 1.0.3)

dser: Implements dendrogram seriation. Interface to DendSer.

Description

Implements dendrogram seriation. Interface to DendSer.

Usage

dser(x, ser_weight, cost = costBAR, ...)
# S3 method for data.frame
dser(x, ser_weight, cost = costBAR, ...)
# S3 method for matrix
dser(x, ser_weight, cost = costBAR, scale = TRUE, dmethod = "euclidean", ...)
# S3 method for dist
dser(x, ser_weight, cost = costBAR, hmethod = "average", ...)
# S3 method for hclust
dser(x, ser_weight, cost = costBAR, ...)

Value

Numeric vector giving an optimal dendrogram order

Arguments

x

Used to select method.

ser_weight

Seriation weights. For cost=costLS, defaults to first column of matrix x, otherwise to symmetric matrix version of dist d.

cost

Current choices are costLS, costPL, costLPL, costED, costARc, costBAR.

...

Other args

scale

Logical value,controls whether matrix x should be scaled prior to forming dist.

dmethod

Method of dist calculation. See function dist.

hmethod

Method of hclust calculation. See function hclust.

Methods (by class)

• dser(data.frame): dser method

• dser(matrix): dser method

• dser(dist): dser method

• dser(hclust): dser method

Author

Catherine Hurley & Denise Earle

Details

When x is a matrix or data.drame, forms a dist of rows using function dist with method = dmethod. When x is a dist, forms a hclust with method = hmethod which is then reordered.

Examples

	 			

iriss <- scale(iris[,-5])
plotAsColor(iriss,order.row=dser(iriss))



w <- prcomp(iris[,-5],scale=TRUE)$x[,1]
h<- hclust(dist(iriss))
h$order <- ow <- dser(h,w,cost=costLS) # arranges cases along first PC, within dendrogram


# compare re-rordered dendrogram to PC scores, w
dev.new(width=10,height=5)
par(mar=c(0,2,1,1))
layout(matrix(1:2, nrow = 2), heights = c(4,1.5) )
par(cex=.7)
plot(h,main="",xlab="",hang=-1,labels=FALSE)
u <- par("usr")
par(mar=c(1,2,0,1))
 

plot.new()
par(usr=c(u[1:2],min(w),max(w)))

x<- 1:length(w)
rect(x-.5,0,x+.5,w[ow],col=cutree(h,3)[ow]+1)