Update results for L50 and L100

[ArtPoon]

• revise supplementary figures of MDS plots
• get PERMANOVA results for exposed/enveloped interaction
• PERMANOVA for virus families (not each family)

[ArtPoon]

# average distances among replicates for L=50
load("L50.RData")  # provides `wmat` and `mdatx`
idxs <- sapply(split(1:nrow(mdatx), mdatx$key), function(x) {
  if (length(x)==1) { rep(x, 10) } else { x }
})
# reconstitute distance matrices
res <- lapply(1:10, function(z) {
  idx <- idxs[z, ]
  wmat[idx, idx]
})

# average Wasserstein distances for replicates per alignment (centroids)
wmat.50 <- Reduce("+", res) / length(res) 
mdat.50 <- mdatx[idxs[1,], ]  # reduce metadata to match

mds.50 <- cmdscale(wmat.50)  # generate MDS

[ArtPoon]

you can replace L50.RData with L100.RData and the code will still work @hugocastelan

[ArtPoon]

PERMANOVA is run on wmat.50 or wmat.100

[ArtPoon]

You can get the RData files here: https://zenodo.org/records/17795003