Show dendrogram node values in R
I am using the hclust function:
points <- data.frame(ID = c('A','B','C','D','E'),
x = c(3,4,2.1,4,7),
y = c(6.1,2,5,6,3))
d <- dist(as.matrix(points[, 2:3]))
clusters <- hclust(d,method = "complete")
plot(clusters, labels=points$ID)
Is there a way to show the values at which the points are connected (or the node values (where the difference between samples is minimal))?
I want my plot to look like the picture.
Note. The values shown on the dendrogram are not correct.
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My R package TBEST has a function that can add two color annotations to the hclust object. For your convenience, I am pasting the codes below, so you can use them independently of any packages.
hc2axes<-function (x) {
A <- x$merge
n <- nrow(A) + 1
x.axis <- c()
y.axis <- x$height
x.tmp <- rep(0, 2)
zz <- match(1:length(x$order), x$order)
for (i in 1:(n - 1)) {
ai <- A[i, 1]
if (ai < 0)
x.tmp[1] <- zz[-ai]
else x.tmp[1] <- x.axis[ai]
ai <- A[i, 2]
if (ai < 0)
x.tmp[2] <- zz[-ai]
else x.tmp[2] <- x.axis[ai]
x.axis[i] <- mean(x.tmp)
}
return(data.frame(x.axis = x.axis, y.axis = y.axis))
}
plot_height<-function (hc, height, col = c(2, 3), print.num = TRUE, float = 0.01, cex = NULL, font = NULL)
{
axes <- hc2axes(hc)
usr <- par()$usr
wid <- usr[4] - usr[3]
bp <- as.character(round(height,2))
rn <- as.character(1:length(height))
bp[length(bp)] <- "height"
rn[length(rn)] <- "edge #"
a <- text(x = axes[, 1], y = axes[, 2] + float * wid, bp,
col = col[1], pos = 2, offset = 0.3, cex = cex, font = font)
if (print.num) {
a <- text(x = axes[, 1], y = axes[, 2], rn, col = col[2],
pos = 4, offset = 0.3, cex = cex, font = font)
}
}
Once you insert these two functions, add one line to build your dendrogram, plot(clusters,labels=points$ID);
cluster_height(clusters,height=clusters$height,print.num=F)
You can also display branch numbers on setting print.num=T
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Here one method is using a package dendextend
.
Convert to hanging dendrogram first
library(dendextend)
dend <- as.dendrogram(clusters) %>% hang.dendrogram()
dend <- dend %>% set_labels(points$ID[dend %>% labels()])
Now we find the x, y values for all internal nodes
xy <- dend %>% get_nodes_xy()
is_internal_node <- is.na(dend %>% get_nodes_attr("leaf"))
is_internal_node[which.max(xy[,2])] <- FALSE
xy <- xy[is_internal_node,]
And now we will build a dendrogram and draw labels with a slight offset
plot(dend)
text(xy[,1]+.2, xy[,2]+.2, labels=format(xy[,2], digits=2), col="red")
This gives the following graph
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