Nothing
plotTree <-
function(treeList, colors=NULL, divisions=NULL, main=NULL, sub="", showTipLabel=TRUE, showNodeLabel=FALSE, displayLegend=TRUE, trees=NULL){
### Fix any old arguments
if(!is.null(trees)){
warning("'trees' is deprecated. It has been replaced with treeList. View the help files for details.")
treeList <- trees
}
if(missing(treeList))
stop("At least one valid tree of type 'phylo' is required inside a list.")
if(displayLegend)
displayLegend(colors, divisions)
### Plot every tree passed
par(cex=.75)
for(i in 1:length(treeList)){
tree <- treeList[[i]]
### Determine what color and size each branch should be
branchData <- getBranchSizes(tree$edge.length, colors, divisions)
### Figure out what we are titleing the plot
if(length(main) == length(treeList)){
main2 <- main[i]
}else if(is.null(main)){
main2 <- names(treeList)[i]
}else{
main2 <- main
}
### Use ape to plot the tree
ape::plot.phylo(tree, type="r", root.edge=FALSE, edge.color=branchData$edgecol, edge.width=branchData$edgewid,
show.tip.label=showTipLabel, show.node.label=showNodeLabel, main=main2, sub=sub)
}
}
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