library(MASS) #load library with MDS functions simdata <- read.table("hclust_in.txt") #read in similarity data dissim <- function(x)(c(36-x)) #convert to dissimilarity data dissimdata <- as.dist(apply(simdata[1:20], c(1,2), dissim)) names = simdata[,21] #read in object names mds1 <- isoMDS(dissimdata, k=1) #non-metric MDS in 1 dimension mds2 <- isoMDS(dissimdata, k=2) #non-metric MDS in 2 dimensions mds3 <- isoMDS(dissimdata, k=3) #non-metric MDS in 3 dimensions #scree plot stress = c(mds1$stress, mds2$stress, mds3$stress) dimensions = c(1, 2, 3) plot (dimensions, stress, type="b", xlab="Number of Dimensions", ylab="Stress") #two-dimensional plot plot(mds2$points,type="n", xlab="Dimension 1", ylab="Dimension 2") text(mds2$points,as.character(names)) #three-dimensional plots plot(mds3$points[,1], mds3$points[,2], type="n", xlab="Dimension 1", ylab="Dimension 2") text(mds3$points[,1], mds3$points[,2], as.character(names)) plot(mds3$points[,1], mds3$points[,3], type="n", xlab="Dimension 1", ylab="Dimension 3") text(mds3$points[,1], mds3$points[,3], as.character(names))