horizontal dendrogram in R with labels

Question

I am trying to draw a dendrogram from the hclust function output. I hope the dendrogram is horizontally arranged instead of the default, which can be obtain by (for example)

require(graphics) hc <- hclust(dist(USArrests), "ave") plot(hc) 

I tried to use as.dendrogram() function like plot(as.dendrogram(hc.poi),horiz=TRUE) but the result is without meaningful labels:

If I use plot(hc.poi,labels=c(...)) which is without the as.dendrogram(), I can pass the labels= argument, but now the dendrogram is vertical instead of horizontal. Is there a way to simultaneously arrange the dendrogram horizontally and assign user-specified labels? Thanks!

Update: as an example from the USArrests dataset, suppose I wanna use the abbreviations of the first two letters of the state names as labels, so that I wanna somehow pass labs into the plotting function:

labs = substr(rownames(USArrests),1,2)

which gives

 [1] "Al" "Al" "Ar" "Ar" "Ca" "Co" "Co" "De" "Fl" "Ge" "Ha" [12] "Id" "Il" "In" "Io" "Ka" "Ke" "Lo" "Ma" "Ma" "Ma" "Mi" [23] "Mi" "Mi" "Mi" "Mo" "Ne" "Ne" "Ne" "Ne" "Ne" "Ne" "No" [34] "No" "Oh" "Ok" "Or" "Pe" "Rh" "So" "So" "Te" "Te" "Ut" [45] "Ve" "Vi" "Wa" "We" "Wi" "Wy" 

Answer 1

To show your defined labels in horizontal dendrogram, one solution is to set row names of data frame to new labels (all labels should be unique).

require(graphics) labs = paste("sta_",1:50,sep="") #new labels USArrests2<-USArrests #new data frame (just to keep original unchanged) rownames(USArrests2)<-labs #set new row names hc <- hclust(dist(USArrests2), "ave") par(mar=c(3,1,1,5))  plot(as.dendrogram(hc),horiz=T) 

EDIT - solution using ggplot2

labs = paste("sta_",1:50,sep="") #new labels rownames(USArrests)<-labs #set new row names hc <- hclust(dist(USArrests), "ave")  library(ggplot2) library(ggdendro)  #convert cluster object to use with ggplot dendr <- dendro_data(hc, type="rectangle")   #your own labels (now rownames) are supplied in geom_text() and label=label ggplot() +    geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) +    geom_text(data=label(dendr), aes(x=x, y=y, label=label, hjust=0), size=3) +   coord_flip() + scale_y_reverse(expand=c(0.2, 0)) +    theme(axis.line.y=element_blank(),         axis.ticks.y=element_blank(),         axis.text.y=element_blank(),         axis.title.y=element_blank(),         panel.background=element_rect(fill="white"),         panel.grid=element_blank()) 

Answer 2

Using dendrapply you can customize your dendro as you like.

colLab <- function(n) {   if(is.leaf(n)) {     a <- attributes(n)     attr(n, "label") <- substr(a$label,1,2)             #  change the node label      attr(n, "nodePar") <- c(a$nodePar, lab.col = 'red') #   change the node color   }   n }  require(graphics) hc <- hclust(dist(USArrests), "ave") clusDendro <- as.dendrogram(hc) clusDendro <- dendrapply(clusDendro, colLab) op <- par(mar = par("mar") + c(0,0,0,2)) plot(clusDendro,horiz=T)