Integrating OTU abundance heatmap and collapsed tree

[Chun-Hui Gao]

Hi,

I have a microbiome dataset, and want to show the species abundance with phylogenic tree. 

# random tree of OTUs

set.seed(0)

tr <- rtree(100)

# taxnomy of the OTUs

tax <- data.frame(name = sample(tr$tip.label),

                  phylum = sapply(sample(1:3,Ntip(tr),replace = TRUE), function(x) paste("phylum",x,sep="_")),

                  class = sapply(sample(1:10,Ntip(tr),replace = TRUE), function(x) paste("class",x,sep="_")),

                  family = sapply(sample(1:12,Ntip(tr),replace = TRUE), function(x) paste("family",x,sep="_")),

                  genus = sapply(sample(1:20,Ntip(tr),replace = TRUE), function(x) paste("genus",x,sep="_"))

                  )

# species abundance of the OTUs in samples

data <- data.frame(matrix(runif(600),ncol=6),row.names = sample(tr$tip.label))

p <- ggtree(tr) + geom_tiplab(align = TRUE)

gheatmap(p,data)

This can be done by these codes and give a figure like this.

But what I want is more. Since these OTUs are group to different phylum, class, family and genus, it may give more information by collapsed tree leaves at a given phylogenic level, for example genus. 

I draw a picture to show this thought, but don't know how to do using R + ggtree.

This picture shows: 1) OTUs in this tree were collapsed at genus level. 2) the genus nodes were shaped and/or colored by different genus. 3) name of genus were used as label. 4) heatmap of three genus were integrated with the tree.