do.idmap {Rdimtools}

Interactive Document Map

Description

Interactive Document Map originates from text analysis to generate maps of documents by placing similar documents in the same neighborhood. After defining pairwise distance with cosine similarity, authors asserted to use either NNP or FastMap as an engine behind.

Usage

do.idmap(
  X,
  ndim = 2,
  preprocess = c("null", "center", "scale", "cscale", "whiten", "decorrelate"),
  engine = c("NNP", "FastMap")
)

Arguments

X

an (n\times p) matrix or data frame whose rows are observations and columns represent independent variables.

ndim

an integer-valued target dimension.

preprocess

an additional option for preprocessing the data. Default is "null". See also aux.preprocess for more details.

engine

either NNP or FastMap.

Value

a named list containing

Y

an (n\times ndim) matrix whose rows are embedded observations.

trfinfo

a list containing information for out-of-sample prediction.

References

Minghim R, Paulovich FV, de Andrade Lopes A (2006). “Content-Based Text Mapping Using Multi-Dimensional Projections for Exploration of Document Collections.” In Erbacher RF, Roberts JC, Gröhn MT, Börner K (eds.), Visualization and Data Analysis, 60600S.

See Also

do.nnp, do.fastmap

Examples

## load iris data
data(iris)
set.seed(100)
subid = sample(1:150,50)
X     = as.matrix(iris[subid,1:4])
lab   = as.factor(iris[subid,5])

## let's compare with other methods
out1 <- do.pca(X, ndim=2)
out2 <- do.lda(X, ndim=2, label=lab)
out3 <- do.idmap(X, ndim=2, engine="NNP")

## visualize
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,3))
plot(out1$Y, pch=19, col=lab, main="PCA")
plot(out2$Y, pch=19, col=lab, main="LDA")
plot(out3$Y, pch=19, col=lab, main="IDMAP")
par(opar)