Combining a heatmap and a dendrogram in a grob plot

Question

I'm trying to plot a heatmap along with a row dendrogram, which I manipulated (pruned the number of branches), aligned using grid.draw.

Here's my data:

set.seed(10)
mat     <- matrix(rnorm(24*10,mean=1,sd=2),nrow=24,ncol=10,dimnames=list(paste("g",1:24,sep=""),paste("my.expriment.sample",1:10,sep="")))
dend    <- as.dendrogram(hclust(dist(mat)))
row.ord <- order.dendrogram(dend)
mat     <- matrix(mat[row.ord,],nrow=24,ncol=10,
             dimnames=list(rownames(mat)[row.ord],colnames(mat)))
mat.df  <- reshape2::melt(mat,value.name="expr",varnames=c("gene","sample"))

The heatmap part of the plot:

require(ggplot2)
map.plot <- ggplot(mat.df,aes(x=sample,y=gene)) + geom_tile(aes(fill=expr)) +
    scale_fill_gradient2("expr",high="darkred",low="darkblue") + theme_bw() + 
    theme(legend.key=element_blank(),legend.position="right", axis.text.y=element_blank(), axis.ticks.y=element_blank(), 
    panel.border=element_blank(), strip.background=element_blank(),  axis.text.x=element_text(angle=45,hjust=1,vjust=1), 
    legend.text=element_text(size=5), legend.title=element_text(size=8), legend.key.size=unit(0.4,"cm"))

Which gives:

Notice the long column labels - that's similar to what I have in reality.

Here's how I manipulate and plot the dendrogram:

depth.cutoff <- 11
dend <- cut(dend,h=depth.cutoff)$upper
require(dendextend)
gg.dend <- as.ggdend(dend)

#change vertical segments that lead to leaves
distinctColors <- function(n) {
  if (n <= 8) {
    res <- brewer.pal(n, "Set2")
  } else {
    res <- hcl(h=seq(0,(n-1)/(n),length=n)*360,c=100,l=65,fixup=TRUE)
  }
}

cluster.cols <- distinctColors(nrow(gg.dend$labels))
leaf.heights <- dplyr::filter(gg.dend$nodes,!is.na(leaf))$height
leaf.seqments.idx <- which(gg.dend$segments$yend %in% leaf.heights)
gg.dend$segments$yend[leaf.seqments.idx] <- max(gg.dend$segments$yend[leaf.seqments.idx])
gg.dend$segments$col[leaf.seqments.idx] <- cluster.cols

#change labels
gg.dend$labels$label <- 1:nrow(gg.dend$labels)
gg.dend$labels$y <- max(gg.dend$segments$yend[leaf.seqments.idx])
gg.dend$labels$x <- gg.dend$segments$x[leaf.seqments.idx]
gg.dend$labels$col <- cluster.cols
dend.plot <- ggplot(gg.dend,labels=F)+scale_y_reverse()+coord_flip()+annotate("text",size=10,hjust=0,x=gg.dend$label$x,y=gg.dend$label$y,label=gg.dend$label$label,colour=gg.dend$label$col)

which gives:

Trying to follow this example, I do:

require(gtable)
plot.grob <- ggplotGrob(dend.plot)
plot.grob <- gtable_add_cols(plot.grob,unit(1,"cm"))
plot.grob <- gtable_add_grob(plot.grob,ggplotGrob(map.plot),t=1,l=ncol(plot.grob),b=1,r=ncol(plot.grob))
grid.newpage()
grid.draw(plot.grob)

But this comes out messed up:

Any idea how to get dend.plot aligned with the heatmap part of map.plot such that the lower branch of dend.plot is bottom aligned with the the heatmap and not the bottom of the column labels?

Error in labs(y = lab.row, x = lab.col) : object 'lab.row' not found — Axeman
It would seem more straightforward to add the dendrogram to the heatmap's gtable — baptiste
A lot is going on in your question. (1) consider using dendextend::color_branches (2) generally you can combine a dendrogram with a heatmap (such as in gplots::heatmap.2) by supplying your dendrogram to the Rowv parameter. You can see that in these examples here: cran.r-project.org/web/packages/dendextend/vignettes/… (3) lastly, have a look at the heatmaply package: cran.r-project.org/web/packages/heatmaply/vignettes/… — Tal Galili

Axeman Axeman · Accepted Answer · 2017-02-03T09:05:47

cowplot is super good at aligning ggplots.

library(cowplot)
plot_grid(dend.plot, map.plot, align = 'h')

Also, try to have a bit shorter example (why do I need a super detailed theme call?), and make sure it actually runs in a clean session.

Combining a heatmap and a dendrogram in a grob plot

1 Answers