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I'm currently constructing a dendrogram and I'm using 'dendextend' to tweak the look of it. I've been able to do everything I want to (labelling leaves and highlighting branches of my chosen clusters), except drawing rectangles around pre-defined clusters.

My data (which can be sourced from this file: Barra_IBS_example.matrix) was clustered with 'pvclust', so 'pvrect' draws the rects in the correct position, but it cuts the labels (see image below), so I want to reproduce it with 'rect.dendrogram', however, I can't figure out how to tell the function to use the clustering data from 'pvclust'.

dendrogram with pvrect

This is the code I'm using:

idnames <- dimnames(ibs_mat)[[1]] ibs.pv <- pvclust(ibs_mat, nboot=1000) ibs.clust <- pvpick(ibs.pv, alpha=0.95) names(ibs.clust$clusters) <- paste0("Cluster", 1:length(ibs.clust$clusters)) # Choose a colour palette pal <- brewer.pal(length(ibs.clust$clusters), "Paired") # Transform the list to a dataframe ibs_meta <- bind_rows(lapply(names(ibs.clust$clusters), function(l) data.frame(Cluster=l, Sample = ibs.clust$clusters[[l]]))) # Add the rest of the non-clustered samples (and assign them as Cluster0), add colour to each cluster ibs_table <- ibs_meta %>% rbind(., data.frame(Cluster = "Cluster0", Sample = idnames[!idnames %in% .$Sample])) %>% mutate(Cluster_int=as.numeric(sub("Cluster", "", Cluster))) %>% mutate(Cluster_col=ifelse(Cluster_int==0, "#000000", pal[Cluster_int])) %>% .[match(ibs.pv$hclust$labels[ibs.pv$hclust$order], .$Sample),] hcd <- as.dendrogram(ibs.pv) %>% #pvclust_show_signif(ibs.pv, show_type = "lwd", signif_value = c(2, 1),alpha=0.25) %>% set("leaves_pch", ifelse(ibs_table$Cluster_int>0,19,18)) %>% # node point type set("leaves_cex", 1) %>% # node point size set("leaves_col", ibs_table$Cluster_col) %>% #node point color branches_attr_by_labels(ibs_meta$Sample, TF_values = c(2, Inf), attr = c("lwd")) %>% # change branch width # rect.dendrogram(k=12, cluster = ibs_table$Cluster_int, border = 8, lty = 5, lwd = 1.5, # lower_rect = 0) %>% # add rectangles around clusters plot(main="Barramundi samples IBS based clustering") pvrect(ibs.pv, alpha=0.95, lwd=1.5)

Many thanks, Ido

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  • Please provide minimum reproducible data we can run your code on, e.g. paste the output of dput(ibs_mat) or a subset Commented May 29, 2017 at 0:45
  • @R.S. An example file created by dput(ibs_mat) was added in the question. Commented May 29, 2017 at 3:08
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    Where does the idnames function come from, please clear your workspace and rerun your code to make sure everything is included in the above code, include all libraries that need to be installed. Commented May 29, 2017 at 4:44
  • @R.S. the names are simply the matrix names (though in the example they did derived from an external function). I've updated the code above to use the dimnames of the matrix. Commented May 29, 2017 at 12:32

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ok, this took more work than I had hoped, but I got a solution for you.

I created a new function called pvrect2 and just pushed it to the latest version of dendextend on github. Here is a self contained example demonstrating the solution:

devtools::install_github('talgalili/dendextend') library(pvclust) library(dendextend) data(lung) # 916 genes for 73 subjects set.seed(13134) result <- pvclust(lung[, 1:20], method.dist="cor", method.hclust="average", nboot=10) par(mar = c(9,2.5,2,0)) dend <- as.dendrogram(result) dend %>% pvclust_show_signif(result, signif_value = c(3,.5)) %>% pvclust_show_signif(result, signif_value = c("black", "grey"), show_type = "col") %>% plot(main = "Cluster dendrogram with AU/BP values (%)") # pvrect(result, alpha=0.95) pvrect2(result, alpha=0.95) text(result, alpha=0.95)

[1]: https://i.sstatic.net/GUvdV.png

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7 Comments

That's great , many thanks for providing a stable solution and not just a one-time workaround!! Highly appreciated.
My pleasure :) I think it should be generalized to use rect.dendrogram, but I would get to it at another time...
@TalGalili Is it possible to maintain the AU/BP values annotated above the branches from pvclust?
Hi @R.S. you just need to add text(result, alpha=0.95). I've updated the answer accordingly.
Hi @TalGalili, I just came back to your solution (for another dataset this time), but when I tried to control the AU/BP text labels attributes (size, color, rotation), only print.num=FALSE had an effect on the output. My command was: text(result, print.num=FALSE, srt=90, cex.pv=0.6, col.pv=c(2,0,0))
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