Missing Tree Tips When Plotting Phenogram

Question

When I generate a phenogram using the phytools package, the tips and tip labels of the trees are not displaying. Does anyone have any ideas on how to fix this, or another way of plotting a phenogram with nodes and tips with a y axis plotted at the value of the trait in question?

Here's what I have:

midpointData <-
structure(list(Species = structure(1:6, .Label = c("Icterus_croconotus", 
"Icterus_graceannae", "Icterus_icterus", "Icterus_jamacaii", 
"Icterus_mesomelas", "Icterus_pectoralis"), class = "factor"), 
    bio_1nam = c(243L, 193L, 225L, 209L, 189L, 180L), bio_12nam = c(5127.5, 
    751.5, 1373, 914.5, 4043.5, 2623.5), bio_16nam = c(1470.5, 
    442, 656.5, 542, 1392.5, 1074), bio_17nam = c(1094.5, 51.5, 
    135, 189.5, 768.5, 377.5), bio_2nam = c(97.5, 91.5, 83, 82.5, 
    81, 102), bio_5nam = c(314, 265.5, 311, 274, 282, 281), bio_6nam = c(167.5, 
    132.5, 175.5, 154.5, 128, 114)), .Names = c("Species", "bio_1nam", 
"bio_12nam", "bio_16nam", "bio_17nam", "bio_2nam", "bio_5nam", 
"bio_6nam"), class = "data.frame", row.names = c(NA, -6L))

prunedTargetTree <- 
structure(list(edge = structure(c(7L, 7L, 8L, 9L, 9L, 8L, 10L, 
11L, 11L, 10L, 1L, 8L, 9L, 2L, 3L, 10L, 11L, 4L, 5L, 6L), .Dim = c(10L, 
2L)), Nnode = 5L, tip.label = c("Icterus_mesomelas", "Icterus_pectoralis", 
"Icterus_graceannae", "Icterus_croconotus", "Icterus_icterus", 
"Icterus_jamacaii"), edge.length = c(0.152443952069696, 0.014866140819964, 
0.0311847312922788, 0.106393079957453, 0.106393079957453, 0.0727572150872864, 
0.0130293222294024, 0.0517912739330428, 0.0517912739330428, 0.0648205961624452
)), .Names = c("edge", "Nnode", "tip.label", "edge.length"), class = "phylo", order = "cladewise")

library(phytools)
reconBio1 <- ace(midpointData$bio_1nam, prunedTargetTree, type = "continuous", method = "ML")
bio1final <- c(reconBio1$ace, midpointData$bio_1nam)
names(bio1final) <- c(7,8,9,10,11,4,3,5,6,1,2)
plot.new()
phenogram(prunedTargetTree, bio1final, ylim = c(min(bio1final), max(bio1final)))

Here's what the tree looks like: TreeWithoutTips

I'm having trouble understanding how `biolfinal` is "a vector containing the states at the tips or the states at all the tips and the internal nodes of the tree." — IRTFM, Jan 18 '14 at 21:39
My understanding was that each node or tip of the tree prunedTargetTree has a number. The names of each object in bio1final correspond with these nodes or tips. The number associated with that name is the character state at that node. Is that not so? — Hannah O., Jan 19 '14 at 04:20
Reasoning by analogy with the worked example in the help page. it appeared to me that the word "states" in this package was referring to names and I was expecting that the vector would be 'character' rather than 'numeric'. (I'm not a user of that package, nor am I experienced in this domain so at this point I think it would be helpful to provide the code and data that created those objects rather than dropping them in from outer space and expecting everything to fit together.) — IRTFM, Jan 19 '14 at 17:59

score 0 · Accepted Answer · answered Jan 20 '14 at 04:43

I have solved the problem, but wanted to share the solution in case others run into the same issue. pheonogram() looks for names in the argument x (aka bio1final) that match prunedTargetTree$tip.label, not the numeric index of the tip. Instead of:

bio1final <- c(reconBio1$ace, midpointData$bio_1nam); 
names(bio1final) <- c(7,8,9,10,11,4,3,5,6,1,2)

it should read:

bio1final <- c(reconBio1$ace, midpointData$bio_1nam); 
names(bio1final) <- c(7,8,9,10,11,as.character(midpointData$Species))

**as.character is important, because otherwise $Species is read in as a factor, and the tips of the tree still won't plot.

Missing Tree Tips When Plotting Phenogram

1 Answers1