clusplot.default  R Documentation 
Creates a bivariate plot visualizing a partition (clustering) of the data. All observation are represented by points in the plot, using principal components or multidimensional scaling. Around each cluster an ellipse is drawn.
## Default S3 method:
clusplot(x, clus, diss = FALSE,
s.x.2d = mkCheckX(x, diss), stand = FALSE,
lines = 2, shade = FALSE, color = FALSE,
labels= 0, plotchar = TRUE,
col.p = "dark green", col.txt = col.p,
col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,
span = TRUE,
add = FALSE,
xlim = NULL, ylim = NULL,
main = paste("CLUSPLOT(", deparse1(substitute(x)),")"),
sub = paste("These two components explain",
round(100 * var.dec, digits = 2), "% of the point variability."),
xlab = "Component 1", ylab = "Component 2",
verbose = getOption("verbose"),
...)
x 
matrix or data frame, or dissimilarity matrix, depending on
the value of the In case of a matrix (alike), each row corresponds to an observation,
and each column corresponds to a variable. All variables must be
numeric. Missing values ( In case of a dissimilarity matrix, 
clus 
a vector of length n representing a clustering of 
diss 
logical indicating if 
s.x.2d 
a 
stand 
logical flag: if true, then the representations of the n observations in the 2dimensional plot are standardized. 
lines 
integer out of In case E1 and E2 overlap on the line through

shade 
logical flag: if TRUE, then the ellipses are shaded in relation to their density. The density is the number of points in the cluster divided by the area of the ellipse. 
color 
logical flag: if TRUE, then the ellipses are colored with respect to their density. With increasing density, the colors are light blue, light green, red and purple. To see these colors on the graphics device, an appropriate color scheme should be selected (we recommend a white background). 
labels 
integer code, currently one of 0,1,2,3,4 and 5. If
The levels of the vector A possible 
plotchar 
logical flag: if TRUE, then the plotting symbols differ for points belonging to different clusters. 
span 
logical flag: if TRUE, then each cluster is represented by the ellipse with
smallest area containing all its points. (This is a special case of the
minimum volume ellipsoid.) There are also some special cases: When a cluster consists of only
one point, a tiny circle is drawn around it. When the points of a
cluster fall on a straight line, 
add 
logical indicating if ellipses (and labels if 
col.p 
color code(s) used for the observation points. 
col.txt 
color code(s) used for the labels (if 
col.clus 
color code for the ellipses (and their labels); only one if color is false (as per default). 
cex, cex.txt 
character expansion (size), for the point symbols and point labels, respectively. 
xlim, ylim 
numeric vectors of length 2, giving the x and y
ranges as in 
main 
main title for the plot; by default, one is constructed. 
sub 
sub title for the plot; by default, one is constructed. 
xlab, ylab 
x and y axis labels for the plot, with defaults. 
verbose 
a logical indicating, if there should be extra diagnostic output; mainly for ‘debugging’. 
... 
Further graphical parameters may also be supplied, see

clusplot
uses function calls
princomp(*, cor = (ncol(x) > 2))
or
cmdscale(*, add=TRUE)
, respectively, depending on
diss
being false or true. These functions are data reduction
techniques to represent the data in a bivariate plot.
Ellipses are then drawn to indicate the clusters. The further layout of the plot is determined by the optional arguments.
An invisible list with components:
Distances 
When 
Shading 
A vector of length k (where k is the number of clusters), containing the
amount of shading per cluster. Let y be a vector where element i is the
ratio between the number of points in cluster i and the area of ellipse i.
When the cluster i is a line segment, y[i] and the density of the cluster are
set to 
a visual display of the clustering is plotted on the current graphics device.
When we have 4 or fewer clusters, then the color=TRUE
gives
every cluster a different color. When there are more than 4 clusters,
clusplot uses the function pam
to cluster the
densities into 4 groups such that ellipses with nearly the same
density get the same color. col.clus
specifies the colors used.
The col.p
and col.txt
arguments, added for R,
are recycled to have length the number of observations.
If col.p
has more than one value, using color = TRUE
can
be confusing because of a mix of point and ellipse colors.
Pison, G., Struyf, A. and Rousseeuw, P.J. (1999)
Displaying a Clustering with CLUSPLOT,
Computational Statistics and Data Analysis, 30, 381–392.
Kaufman, L. and Rousseeuw, P.J. (1990). Finding Groups in Data: An Introduction to Cluster Analysis. Wiley, New York.
Struyf, A., Hubert, M. and Rousseeuw, P.J. (1997). Integrating Robust Clustering Techniques in SPLUS, Computational Statistics and Data Analysis, 26, 1737.
princomp
, cmdscale
, pam
,
clara
, daisy
, par
,
identify
, cov.mve
,
clusplot.partition
.
## plotting votes.diss(dissimilarity) in a bivariate plot and
## partitioning into 2 clusters
data(votes.repub)
votes.diss < daisy(votes.repub)
pamv < pam(votes.diss, 2, diss = TRUE)
clusplot(pamv, shade = TRUE)
## is the same as
votes.clus < pamv$clustering
clusplot(votes.diss, votes.clus, diss = TRUE, shade = TRUE)
## Now look at components 3 and 2 instead of 1 and 2:
str(cMDS < cmdscale(votes.diss, k=3, add=TRUE))
clusplot(pamv, s.x.2d = list(x=cMDS$points[, c(3,2)],
labs=rownames(votes.repub), var.dec=NA),
shade = TRUE, col.p = votes.clus,
sub="", xlab = "Component 3", ylab = "Component 2")
clusplot(pamv, col.p = votes.clus, labels = 4)# color points and label ellipses
# "simple" cheap ellipses: larger than minimum volume:
# here they are *added* to the previous plot:
clusplot(pamv, span = FALSE, add = TRUE, col.clus = "midnightblue")
## Setting a small *label* size:
clusplot(votes.diss, votes.clus, diss = TRUE, labels = 3, cex.txt = 0.6)
if(dev.interactive()) { # uses identify() *interactively* :
clusplot(votes.diss, votes.clus, diss = TRUE, shade = TRUE, labels = 1)
clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# ident. only points
}
## plotting iris (data frame) in a 2dimensional plot and partitioning
## into 3 clusters.
data(iris)
iris.x < iris[, 1:4]
cl3 < pam(iris.x, 3)$clustering
op < par(mfrow= c(2,2))
clusplot(iris.x, cl3, color = TRUE)
U < par("usr")
## zoom in :
rect(0,1, 2,1, border = "orange", lwd=2)
clusplot(iris.x, cl3, color = TRUE, xlim = c(0,2), ylim = c(1,1))
box(col="orange",lwd=2); mtext("sub region", font = 4, cex = 2)
## or zoom out :
clusplot(iris.x, cl3, color = TRUE, xlim = c(4,4), ylim = c(4,4))
mtext("'super' region", font = 4, cex = 2)
rect(U[1],U[3], U[2],U[4], lwd=2, lty = 3)
# reset graphics
par(op)
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