reproduce phyloseq example using ggtree

phyloseq example

This example is demonstrated in phyloseq vignette.

require(phyloseq)
data(GlobalPatterns)
GP <- prune_taxa(taxa_sums(GlobalPatterns) > 0, GlobalPatterns)
GP.chl <- subset_taxa(GP, Phylum=="Chlamydiae")

plot_tree(GP.chl, color="SampleType", shape="Family", label.tips="Genus", size="Abundance")

reproduce using ggtree

require(ggplot2)
require(ggtree)

tree <- GP.chl@phy_tree
p <- ggtree(tree, ladderize = F)
p <- p + geom_text(subset=.(!isTip), aes(label=label), hjust=-.2, size=4)

dd <- psmelt(GP.chl)
dd <- dd[dd$Abundance > 0, ]
data <- merge(p$data, dd, by.x="label", by.y="OTU")

spacing <- 0.02
idx <- with(data, sapply(table(node)[unique(node)], function(i) 1:i)) %>% unlist
hjust <- spacing * idx * max(data$x)
data$xdodge <- data$x + hjust

p <- p + geom_point(data=data, aes(x=xdodge, color=SampleType, shape=Family, size=Abundance), na.rm=T) + 
         theme(legend.position="right") + scale_size_continuous(trans=log_trans(5))

d2 <- unique(data[, c("x", "y", "Genus")])
p + geom_text(data=d2, aes(label=Genus), hjust=-.3, na.rm=T, size=4)

Although Abundance points were adjusted to prevent overlap, it's hard to detect pattern in this figure.

We believe using gheatmap is more easy to interpret the data.

We can also use dots to encode more information with aligning them vertically by SampleType. This is a better way and more easy to interpret.