mp (version 0.4.1)

forceScheme: Force Scheme Projection

Description

Creates a 2D representation of the data based on a dissimilarity matrix. A few modifications have been made in relation to the method described in the literature: shuffled indices are used to minimize the order dependency factor, only a fraction of delta is used for better stability and a tolerance factor was introduced as a second stop criterion.

Usage

forceScheme(D, Y = NULL, max.iter = 50, tol = 0, fraction = 8, eps = 1e-05)

Arguments

D

A dissimilarity structure such as that returned by dist or a full symmetric matrix containing the dissimilarities.

Y

Initial 2D configuration. A random configuration will be used when omitted.

max.iter

Maximum number of iterations that the algorithm will run.

tol

The tolerance for the accumulated error between iterations. If set to 0, the algorithm will run max.iter times.

fraction

Controls the point movement. Larger values means less freedom to move.

eps

Minimum distance between two points.

Value

The 2D representation of the data.

References

Eduardo Tejada, Rosane Minghim, Luis Gustavo Nonato: On improved projection techniques to support visual exploration of multi-dimensional data sets. Information Visualization 2(4): 218-231 (2003)

See Also

dist (stats) and dist (proxy) for d computation

Examples

# Eurodist example
emb <- forceScheme(eurodist)
plot(emb, type = "n", xlab ="", ylab ="", asp=1, axes=FALSE, main="")
text(emb, labels(eurodist), cex = 0.6)

# Iris example
emb <- forceScheme(dist(iris[,1:4]))
plot(emb, col=iris$Species)