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Hi Steve,<div><br></div><div>I am not sure if this question is related to what you were doing with modifying phylo4d. It comes up in a plot example, where a user might want to plot a tree with particular nodes labeled, but the rest blank. </div><div><br></div><div>The default behavior of the phylo4 constructor is to create a node label. So I got it to work, by erasing these and then adding the ones I want, but it's quite kludgy. </div><div><br></div><div>require(phylobase)</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: 12.0px Helvetica">read.nexus("squamatetree1.nex") -> tree</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">tree4 <- as(tree, "phylo4")</div></div><div><div>smalltree4 <- subset(tree4, mrca=MRCA(tree4, "Wetmorena_haetiana", "Abronia_graminea")) </div><div><br></div><div>If we just change the specific node labels and then plot, we get an ugly mess:</div><div><div><div><div><br></div><div>smalltree4$node.label[1] <- "root"</div><div>smalltree4$node.label[12] <- "Ophisaurus"</div><div>plot(smalltree4, show.node.label=T)</div><div><br></div></div></div></div><div>So we have to erase the contents first and then plot:</div><div><br></div><div>smalltree4$node.label <- vector(mode="character", length=23)</div><div><div>smalltree4$node.label</div><div>smalltree4$node.label[1] <- "root"</div><div>smalltree4$node.label[12] <- "Ophisaurus"</div><div>plot(smalltree4, show.node.label=T)</div></div></div><div><br></div><div>Do you have any thoughts on this?</div><div><br></div><div>Marguerite</div><div><br></div><div></div></body></html>