Hi Martin - I'm continuing with my summer task of finalising a phylogeny, and am now using the Rogue package to plot the position of a new fossil discovery in a Bayesian posterior distribution (and calculating supports using TreeTools - thanks for all these lovely packages).
I think I've come across a bug in RoguePlot, although am happy to be corrected. If I plot using your examplar code:
trees <- list(read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(rogue, (a, (b, (c, (d, (e, f))))));"), read.tree(text = "((rogue, a), (b, (c, (d, (e, f)))));"), read.tree(text = "(a, (b, ((c, d), (rogue, (e, f)))));"), read.tree(text = "(a, (b, ((c, (rogue, d)), (e, f))));"), read.tree(text = "(a, (b, (c, (d, (rogue, (e, f))))));")) plotted <- RoguePlot(trees, "rogue", legend = "topleft", legend.inset = 0.02) PlotTools::SpectrumLegend( "bottomleft", palette = colorRampPalette(c(par("fg"), "#009E73"), space = "Lab")(100), legend = plotted$legendLabels, cex = 0.4 )
I get:
5 trees placing the rogue at the (c,d,(e+f)) polytomy, reflecting the underlying trees. If I then add sort to the RoguePlot command (plotted <- RoguePlot(trees, "rogue", legend = "topleft", legend.inset = 0.02, sort = TRUE)), I get this:
which suggests there are 5 trees that placing the rogue at the root. Despite sorting the tips, I believe these five should still optimise to the (c,d,(e+f)) polytomy. Did I miss something, or is there an issue with branch ordering/colouring when the sort command is used?
Hi Martin - I'm continuing with my summer task of finalising a phylogeny, and am now using the Rogue package to plot the position of a new fossil discovery in a Bayesian posterior distribution (and calculating supports using TreeTools - thanks for all these lovely packages).
I think I've come across a bug in RoguePlot, although am happy to be corrected. If I plot using your examplar code:
trees <- list(read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(a, (b, (c, (rogue, (d, (e, f))))));"), read.tree(text = "(rogue, (a, (b, (c, (d, (e, f))))));"), read.tree(text = "((rogue, a), (b, (c, (d, (e, f)))));"), read.tree(text = "(a, (b, ((c, d), (rogue, (e, f)))));"), read.tree(text = "(a, (b, ((c, (rogue, d)), (e, f))));"), read.tree(text = "(a, (b, (c, (d, (rogue, (e, f))))));")) plotted <- RoguePlot(trees, "rogue", legend = "topleft", legend.inset = 0.02) PlotTools::SpectrumLegend( "bottomleft", palette = colorRampPalette(c(par("fg"), "#009E73"), space = "Lab")(100), legend = plotted$legendLabels, cex = 0.4 )I get:
5 trees placing the rogue at the (c,d,(e+f)) polytomy, reflecting the underlying trees. If I then add sort to the RoguePlot command (plotted <- RoguePlot(trees, "rogue", legend = "topleft", legend.inset = 0.02, sort = TRUE)), I get this:
which suggests there are 5 trees that placing the rogue at the root. Despite sorting the tips, I believe these five should still optimise to the (c,d,(e+f)) polytomy. Did I miss something, or is there an issue with branch ordering/colouring when the sort command is used?