`convertToPhyloseq`: row order is different between input TreeSE and output phyloseq

[RiboRings]

Hi!

After running convertToPhyloseq, I noticed that the original row order is not preserved after conversion.

library(mia)
data("Tengeler2020", package = "mia")

tse <- Tengeler2020
pseq <- convertToPhyloseq(tse)

sum(rownames(tse) != taxa_names(pseq))
[1] 150

head(match(taxa_names(pseq), rownames(tse)))
[1] 135  19  27  84 123 105

I tried reordering the rows of the phyloseq object using otu_table and tax_table, but they seem immutable. Maybe original order can be imposed within convertToPhyloseq function? I am not sure why the order is changing in the first place.

[RiboRings]

Apparently the rows get reordered based on phylo tip labels:

mia/R/convertToPhyloseq.R

Line 154 in 997852c

phyloseq::phy_tree(obj) <- phy_tree

This reordering happens specifically for Tengeler2020, where rownames and tip labels have different orders