suppressMessages(library(gplots)) dat <- as.matrix(read.csv(file="dat.csv", row.names=1)) dist2 <- function(x) as.dist(1-cor(t(x), method="pearson")) hclust1 <- function(x) hclust(x, method = "single") distance <- dist2(dat) cluster <- hclust1(distance) dend <- as.dendrogram(cluster) ## R's default recursion limits will be exceeded when plotting this dendrogram try( gplots:::plot.dendrogram(dend) ) try( heatmap.2(dat, Rowv=dend) ) ## Increase them and try again options("expressions"=20000) gplots:::plot.dendrogram(dend) heatmap.2(dat, Rowv=dend)