R Under development (unstable) (2024-01-28 r85838 ucrt) -- "Unsuffered Consequences"
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> library(phylobase)
> library(ape)

Attaching package: 'ape'

The following object is masked from 'package:phylobase':

    edges

> 
> data(geospiza)
> g1 <- as(geospiza,"phylo4")
> g2 <- geospiza
> 
> par(mfrow=c(1,2))
> plot(g1, show.node.label=TRUE)
> ## be careful with this: works if par("fin")=c(5.56,6.77)
> ##                       fails if par("fin")=c(4.87,6.77)
> ##try(plot(g2,show.node.label=TRUE),silent=TRUE)
> ## Here, R was complaining about a lack of room to plot data
> ## so nothing abnormal. -- TJ
> plot(g2, show.node.label=TRUE)
> 
> 
> ## commented out since phylog objects are deprecated anyway
> ## g2B <- as(extractTree(g2), "phylog")
> ##  Note the numbering differences!
> 
> ## round trip
> g2C <- as(read.tree(text=write.tree(as(g1, "phylo"))), "phylo4")
Warning message:
In asMethod(object) : trees with unknown order may be unsafe in ape
> ## comes back in same order
> try(plot(g1, show.node.label=TRUE))
> try(plot(g2C, show.node.label=TRUE))
> 
> g3 = subset(g2, tips.exclude=c("fuliginosa", "fortis", "magnirostris",
+                  "conirostris", "scandens"))
> plot(extractTree(g3))  ## phylo4
> plot(g3)
> 
> 
> ## Playing with new ways of plotting
> 
> if (FALSE) {
+ if(require(MASS)){
+     dist1 <- cophenetic.phylo(as(g2, "phylo"))
+     mdspos <- isoMDS(dist1)$points
+     par(mfrow=c(2, 2))
+     plot(g1)
+     ## plot(mdspos,type="n")
+     ## text(mdspos[,1],mdspos[,2],abbreviate(rownames(mdspos)))
+     ## cmdpos <- cmdscale(dist1)
+     ## plot(cmdpos,type="n")
+     ## text(cmdpos[,1],cmdpos[,2],abbreviate(rownames(mdspos)))
+ }
+ ## never mind, I don't know how to construct a useful
+ ##  2D color space anyway ...
+ }
> 
> treePlot(g2,plot.at.tip=TRUE,tip.plot.fun=
+          function(x,...) {
+            grid::grid.points(seq(along=x),x)})
> 
> proc.time()
   user  system elapsed 
   2.32    0.32    2.65