Dear Gwennaël,
the bootstrapping function is fine, it is just a problem with the
plotting. Can you try this function, it should work:
plotBSNew - function (tree, BStrees, type = unrooted, bs.col = black,
bs.adj = NULL, ...)
{
prop.clades - function (phy, ..., part = NULL, rooted = FALSE)
{
if (is.null(part)) {
obj - list(...)
if (length(obj) == 1 class(obj[[1]]) != phylo)
obj - unlist(obj, recursive = FALSE)
part - prop.part(obj, check.labels = TRUE)
}
bp - prop.part(phy)
if (!rooted){
bp - postprocess.prop.part(bp)
part - postprocess.prop.part(part) # This line I added!!
}
n - numeric(phy$Nnode)
for (i in seq_along(bp)) {
for (j in seq_along(part)) {
if (identical(bp[[i]], part[[j]])) {
n[i] - attr(part, number)[j]
done - TRUE
break
}
}
}
n
}
if (type == phylogram | type == cladogram) {
if (!is.rooted(tree))
tree2 = midpoint(tree)
plot(tree2, type = type, ...)
}
else plot(tree, type = type, ...)
x = prop.clades(tree, BStrees)
x = round((x/length(BStrees)) * 100)
label = c(rep(, length(tree$tip)), x)
ind - get(last_plot.phylo, envir = .PlotPhyloEnv)$edge[,
2]
if (type == phylogram | type == cladogram) {
root = getRoot(tree)
label = c(rep(0, length(tree$tip)), x)
label[root] = 0
ind2 = matchEdges(tree2, tree)
label = label[ind2]
ind = which(label 0)
if (is.null(bs.adj))
bs.adj = c(1, 1)
nodelabels(text = label[ind], node = ind, frame = none,
col = bs.col, adj = bs.adj, ...)
}
else {
if (is.null(bs.adj))
bs.adj = c(0.5, 0.5)
edgelabels(label[ind], frame = none, col = bs.col,
adj = bs.adj, ...)
}
}
plotBSNew(Cassidinaealnx2pmloptim $tree, Cassidinaepmlbs, type=p)
Regards,
Klaus
On 4/3/12, Gwennaël Bataille gwennael.batai...@uclouvain.be wrote:
Dear all,
I have got some troubles with the ML bootstrapping {phangorn} : I get
zero values...
I already had this problem before, but cannot see what's going wrong here.
The script and fasta file are in the end of the mail.
Any idea ?
Many thanks,
Gwennaël
_
#Import the data make a first NJ tree
Cassidinaealnx2- read.dna(file = Cassidinaealnx.fasta, format =
fasta)
Cassidinaealnxdist- dist.dna(Cassidinaealnx2, model = K80,
pairwise.deletion = FALSE)
Cassidinaetrx- nj(Cassidinaealnxdist)
plot(Cassidinaetrx)
Cassidinaertrx- root(Cassidinaetrx, Imatidiumthoracicum)
#ML
Cassidinaealnx2pml- pml(Cassidinaertrx, as.phyDat(Cassidinaealnx2))
Cassidinaealnx2pmloptim- optim.pml(Cassidinaealnx2pml, optNni=TRUE)
plot(Cassidinaealnx2pmloptim)
Cassidinaepmlbs- bootstrap.pml(Cassidinaealnx2pmloptim, optNni=TRUE)
plotBS(Cassidinaealnx2pmloptim $tree, Cassidinaepmlbs, type=p)
Cassidinaealnx.fasta
Agroiconotapropinqua
tganaaaccgaa-ggatcg-aataaattcattcgcg-tttcgattgtcagcgttgagcgg-ttgtgtgactgacggagtacgcttcg-tccgcaccttcagttcatcga-act-ggcttcgaacgcgtgcac-tagtaggacgtcgcgatccg-ttgggcgtcggtctaaggcttgcgg-tggagctcgcgtg--gacgtttc--ggcgtt--ccgcacgaacccgcaatgtccc-gatcgactcgctcgacggt-ata-aagatggcgcccgctactcagttagcgttcgacctacggca-agc-acgtccggtgttt--gatggcn-atcagacctggtcggatcctgtcctc-ggacgactgttgg--ctcgtantg-ttctcgaacagacctcg-ttkaaacgcc-catctgcgacgcgctt-tgggtactttca-ggacccgtcttgaaacacgg-
Microctenochiracumulata
---ctgagaamccgaa-agatcg-aataaattcattcgcg-tttcgattgtcagcgttgagcgg-ttgtgtgactgacggagtacgcttcg-tccgcaccttcagttcatcga-act-ggcttcgaacgcgtgcac-tagtaggacgtcgcgatccg-ttgggcgtcggtctaaggcttgcgg-tggagctcgcgtg--gacgtttc--ggcgt---ccgcacgaacccgcaatgtccc-gatcgacacgctcgacggt-aca-aagatggcgcccgctattcagttagcgttcgacctatggca-agc-acgtccggtgttt--gatggcg-atcagacctggtcggatcccgtcctc-ggacgactgttgg--ctcgtagtg-ttctcgaacagacctcg-ttgaaacgcc-gatctgcgacgctatagctt-tgggtactttca-ggacccgtcttgaaacacg--
Charidotellasexpunctata
--a-tcg-aataaattcatkggcg-tttcgattgtcagcgttggacgg-ttgtgtgactgacggagtacgcttcg-tccgcaccttcagttcatcga-act-ggcttcgaacgcgtgcac-tagtaggacgtcgcgatccg-ttgggcgtcgatctaaggcttgcgg-tggagctcgcgtg--gacgtttc--ggcgtt--ccacacgaacctgcaatgtccc-gatcgactcgctcgacggt-ata-aagatggcgcccgctattcagttagcgttcggcctacggca-agc-acgtgcggtattt--gatggcg-atcagacctggtcggatcccgtcgcc-ggacgactgttgg--ctcgtagtg-ttctcgaacagacctcg-ttgaaacgcc-gatctgcgacgctntagctt-tgggtactttca-ggacccgtcttgaaacacggcagg-
Charidotellasinuata
