plot.constr.hclust: Plotting Method For Space- And Time-Constrained Clustering

In adespatial: Multivariate Multiscale Spatial Analysis

Plotting Method For Space- And Time-Constrained Clustering

Description

Method plot.constr.hclust displays the results of space-constrained or time-constrained agglomerative cluster analyses obtained from multivariate dissimilarity matrices.

Usage

## S3 method for class 'constr.hclust'
plot(x, k, xlim, ylim, xlab, ylab, bg, col,
lty, lwd, col.links, links=FALSE, points=TRUE, pch=21L,
hybrids=c("change","single","none"), lty.hyb=1L, lwd.hyb=1, col.hyb="black",
plot=TRUE, axes=TRUE, cex=1, lwd.pt=1, invert.axes=FALSE, ...)

Arguments

x	A constr.hclust-class object.
k	The number of clusters to delineate.
xlim	Optional: limits, in abscissa, of the zone to be plotted.
ylim	Optional: limits, in ordinate, of the zone to be plotted.
xlab	Optional: labels for x axis annotation.
ylab	Optional: labels for y axis annotation.
bg	Optional: a colour or set of colours to be used for the point backgrounds (one for each of the k clusters), see Details.
col	Optional: a colour or set of colours to be used for the point outlines (defaults to "black" when omitted).
lty	Optional: reference line type (see graphical parameters for details).
lwd	Optional: reference line width (see graphical parameters for details).
col.links	Optional: a colour or set of colours to be used for the links within a cluster (defaults to the point background colours when omitted).
links	Should segments be drawn to represent the edges (links) (default: FALSE).
points	Should observation points be drawn (default: TRUE).
pch	Point character to display observations (default: 21, a circle with a background colour).
hybrids	How should hybrid segments be drawn (default: "change").
lty.hyb	Line type to use for hybrid segments (default: lty).
lwd.hyb	Width of hybrid segments with respect to lwd (default: 1).
col.hyb	Colour of hybrid segments, when applicable (default: "black").
plot	Should a new plotting window be opened first (default: TRUE).
axes	Should the axes be displayed (default: TRUE).
cex	Text and symbol magnification (see graphical parameters) (default: 1).
lwd.pt	Line width around points with respect to lwd (default: 1).
invert.axes	Should axes be inverted on the plot (default: FALSE).
...	Other graphical parameters.

Details

The plotting method uses the coordinates provided by the user of constr.hclust to display the observations. It cuts the tree (see cutree) into k clusters and displays each cluster using the indices returned by cutree. The point background colours can be provided using argument bg. When they are omitted, default colours are provided automatically by the function as either a set of mutually contrasting colours (when k <= 10) or rainbow colours (when k > 10). When links = TRUE, each edge is displayed as a segment with a colour corresponding to the identity of the clusters located at its ends. A special treatment is done for hybrids edges: those whose ends lie in different clusters; it is controlled by argument hybrids. When argument hybrids="change" (the default), hybrid links are represented as segments whose colours change halfway. When hybrids="single", hybrid edges are shown as single-color lines, whose color is given as argument col.hyb, whereas hybrids="none" suppresses the drawing of hybrid edges. Whenever hybrid edges are displayed, their width with respect to the lwd value is controlled by argument lwd.hyb.

When argument plot=FALSE, no plot command is issued and the points (and segments when links = TRUE) are drawn over an existing plotting window. This functionality is to allow one to plot the result of a constrained clustering over an existing map. In that case, arguments xlim, ylim, axes, and all other graphical parameters to which the method plot would responds are ignored.

When disjoint clusters are present (i.e., when the graph provided to constr.hclust is not entirely connected), the function does not allow one to plot fewer clusters than the number of disjoint subsets; a warning message is issued to notify the user.

Author(s)

Guillaume Guénard [e-mail] and Pierre Legendre [e-mail]

Examples

## Artificial map data from Legendre & Legendre (2012, Fig. 13.26)
## n = 16

dat <- c(41,42,25,38,50,30,41,43,43,41,30,50,38,25,42,41)
coord.dat <- matrix(c(1,3,5,7,2,4,6,8,1,3,5,7,2,4,6,8,
                      4.4,4.4,4.4,4.4,3.3,3.3,3.3,3.3,
                      2.2,2.2,2.2,2.2,1.1,1.1,1.1,1.1),16,2)

## Obtaining a list of neighbours:
library(spdep)
listW <- nb2listw(tri2nb(coord.dat), style="B")
links.mat.dat <- listw2mat(listW)
neighbors <- listw2sn(listW)[,1:2]

## Calculating the (Euclidean) distance between points:
D.dat <- dist(dat)

## Display the points:
plot(coord.dat, type='n',asp=1)
title("Delaunay triangulation")
text(coord.dat, labels=as.character(as.matrix(dat)), pos=3)
for(i in 1:nrow(neighbors))
    lines(rbind(coord.dat[neighbors[i,1],],
          coord.dat[neighbors[i,2],]))

## Clustering with a contiguity constraint described by a list of
## links:
grpWD2cst_constr_hclust <-
    constr.hclust(
        D.dat, method="ward.D2",
        neighbors, coord.dat)

## Plot the results with k=5 clusters on a map:
plot(grpWD2cst_constr_hclust, k=5, links=TRUE, las=1,
     xlab="Eastings", ylab="Northings", cex=3, lwd=3)

## Repeat the plot with other values of k (number of groups)

adespatial documentation built on Sept. 11, 2024, 7:04 p.m.