Hi Emmanuel, Rafael, & Elizabeth.

`Some phytools functions suffer from the precisely the same issue`

`identified by Elizabeth as phytools::plotTree and phytools::plotSimmap`

`also have a plot=FALSE option, & Rafael's solution seems to work. For`

`instance, I posted an example to my blog here:`

http://blog.phytools.org/2017/09/possible-solution-for-functions-that.html

`I'm not sure if this means I won't run into difficulty with this`

`solution, but I'm eager to hear why.`

- Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 9/26/2017 11:52 AM, Emmanuel Paradis wrote:

Hi Rafael, This is used in example(phydataplot), but once you called plot(tree, plot = FALSE), you cannot change x.lim, y.lim, etc. You can notice in these examples that these parameters are (most of the time) not nicely set: this is because the data are simulated. If you work interactively, it's quite easy to find the appropriate value of x.lim with a few tries for a given data set. Then, once this is saved in a script, it's possible to repeat the plot and adjust the other parameters (colours, legend, ...) Best, Emmanuel Le 26/09/2017 à 18:10, Rafael Maia a écrit :Hi Elizabeth, I ran into a similar problem recently (with another package) and a simple solution that worked for me is to call par(new=TRUE) before your plot=TRUE plot. So something like: pdf('test.pdf') plot(tree, plot=FALSE) par(new=TRUE) plot(tree, plot=TRUE) dev.off() HTH Best, Rafael Maia — Junior Fellow, Simons Society of Fellows Rubenstein Lab, Columbia University Department of Ecology, Evolution and Environmental Biology New York, NY http://www.rafaelmaia.netOn Sep 26, 2017, at 9:03 AM, Emmanuel Paradis <emmanuel.para...@ird.fr <mailto:emmanuel.para...@ird.fr>> wrote: Hi Elizabeth, You can use directly the functions behind the calculations of the coordinates; they are documented together: ?node.depth. But this will not give the final coordinates since more calculations are needed depending on the widths of the labels, etc. Another possibility could be to plot the tree in a temporary file and get the settings afterwards, eg: R> tmpf <- tempfile() R> pdf(tmpf) R> plot(rtree(100)) R> dev.off() X11cairo 2 R> lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv) R> lastPP $type [1] "phylogram" .... R> unlink(tmpf) # optional since it's deleted when R is closed Just for the record, if some users wonder about the usefulness of the option plot=FALSE, see some examples in: example(phydataplot) HTH Best, Emmanuel Le 26/09/2017 à 14:58, Elizabeth Purdom a écrit :Hello, I am writing a function that calls plot.phylo in the ape package with the option plot=FALSE. I then do some calculations with the output (the calculated coordinates), and then make another call to plot.phylo with plot=TRUE. If I do this, then the plot=FALSE option creates a blank plot, which is the result that is clearly documented in the help pages. However, I do not want this blank plot, because I am saving the result (the second call to plot.phylo) to a pdf, and so the pdf has a blank page before the plot I want. And since I’m calling this in a function, I can’t “wait” for the second plot (a similar problem occurs if you run it in a knitr document) Is there a way to get the output from plot.phylo with all of the coordinates, etc. without having to have the blank plot? (I do not want an option to “add” the plot to the blank plot, if it exists, because I am doing these calculations so that in my next call I can change the x.lim options so the tree only takes up a fraction of the plot, so I need to reset the par, etc., and not just draw on the original coordinates set up by the blank plot) Thank you, Elizabeth Purdom Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/302lu3ZCAL7_______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org <mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/_______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

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