I created a gene distance matrix, based on GO terms similarity (using the R package GOSemSim).

I am then basically doing the following, where gene_dist is my distance matrix:

plot(hclust(gene_dist, method="average"))

I don't understand why the displayed tree from plot.hclust is not ultrametric, even though "average" agglomeration is UPGMA. The similarities from GOSemSim::mgeneSim (measure "Wang", combine "Best Matching Average") are likely not producing euclidean distances, but that shouldn't matter.

Also, if I use the library ape for plotting:

library(ape)
plot(as.phylo(hclust(gene_dist, method="average")))

It shows as ultrametric. Why? Is it just a display choice?

Here is some reproducible example code:

library(GOSemSim)

examplelist <- c("ZNF575", "GALNT11", "GJC3", "POLRMT", "PKDCC", "COL18A1", "INS-IGF2", "IQSEC1", "CFC1", "OPA3")
hsGOex <- godata('org.Hs.eg.db', ont='BP', computeIC=F, keytype='SYMBOL')
gene_sim_ex <- mgeneSim(genes=examplelist, semData=hsGOex, measure='Wang', combine='BMA')
isSymmetric(gene_sim_ex)
## [1] TRUE

gene_dist_ex <- as.dist(1 - gene_sim_ex)
labels(gene_dist_ex)
## [1] "GALNT11" "POLRMT"  "PKDCC"   "COL18A1" "IQSEC1"  "CFC1"    "OPA3"

plot(hclust(gene_dist_ex, method="average"))

library(ape)
dev.new()
plot(as.phylo(hclust(gene_dist_ex, method="average")))
axisPhylo()