Hello, many thanks, now it works. Bests, Ivett
2014-07-28 1:19 GMT+02:00 Liam J. Revell <liam.rev...@umb.edu>: > Hi Ivett. > > x.lim & y.lim for type="fan" still work. In this case the standard > dimensions are just +- the total tree length & space for labels, so you > could try (for instance): > > h<-max(nodeHeights(tree)) > plot(tree,type="fan",no.margin=TRUE,x.lim=1.2*c(-h,h)) > > and then make further adjustments as necessary. > > All the best, Liam > > > Liam J. Revell, Assistant 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 7/27/2014 3:40 PM, Ivett Pipoly wrote: > >> Hi, >> thanks a lot for the answers. >> I have a few additional information. >> I use the type="fan" argument, so my tree is round-shaped, so I can not >> exactly set the xlim and ylim... >> I.e my tree is: plot.phylo(tree4, type = "fan", cex = 0.6, no.margin = >> T, font = 1, use.edge.length = T, label.offset = 0.15). I set the >> margins like: par(mar=c(0,0,0,0),oma=c(0,0,0,0)), and I made a .tiff >> image with tiff(filename="tree1.tif",width = 18.30, height = 18.30, >> units = "cm", res=600) >> I tried to do as the advice said but the species names are still not fit >> in the picture. I there any arguments to set the size of the topology of >> the tree? Or can I set the size of the tree? >> >> PS: My problem with the two lines of symbols is solved, thanks. >> >> Best wishes, >> Ivett Pipoly >> >> >> >> 2014-07-27 17:05 GMT+02:00 Emmanuel Paradis <emmanuel.para...@ird.fr >> <mailto:emmanuel.para...@ird.fr>>: >> >> >> Hi Ivett, >> >> Following Eliot's and Liam's replies, I wish to add a few points. >> >> plot(mytree, no.margin = TRUE) is the same than: >> >> par(mar = rep(0, 4)) >> plot(mytree) >> >> So the margins are effectively removed and, logically, you cannot >> draw something in there. >> >> Liam pointed you in the right direction: you have to manage space >> around the tree by setting x.lim with one (more space on the right >> of the tree) or two (more space on both sides) values. Note this >> option (and y.lim too) manages space around the tree within the plot >> region, not in the marings. >> >> The x and y limits of the plot are indeed set by default but this is >> much less easy than it may seem. That's why it's always good to play >> with x.lim and/or y.lim (also label.offset) to see if the graph may >> look better. Besides, if one wants to add graphical elements, the >> correct values of these options cannot be found a priori; see >> example(phydataplot). >> >> The output depends also on the size of the graphical device you use. >> If you are making a figure with lots of elements, it may be worth >> writing it directly in PDF of sufficient size, eg: >> >> pdf("mytree.pdf", width = 30, heigth = 20) >> plot(mytree, .... >> tiplabels(.... >> .... >> dev.off() >> >> To draw several series of symbols with tiplabels, you can play with >> the option 'adj': there is an example in example(nodelabels). >> >> HTH >> >> Emmanuel >> >> Le 25/07/2014 19:52, Liam J. Revell a écrit : >> >> See comments below. I hope the instructions are helpful. >> >> Liam J. Revell, Assistant Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.__revell/ >> <http://faculty.umb.edu/liam.revell/> >> email: liam.rev...@umb.edu <mailto:liam.rev...@umb.edu> >> >> blog: http://blog.phytools.org >> >> On 7/25/2014 1:27 PM, Eliot Miller wrote: >> >> My first problem: I can not set the margins of the plot, >> because when >> I use >> >> the adequate label.offset value to fit the symbols >> between branches and >> names, the names of the species are not fit in the plot >> (the end of the >> names are disappear). >> >> >> Your plotting window should be automatically resized when you >> increase >> label.offset, although I'm not sure this is true for all versions >> of >> ape. Are you sure you are working with the latest version (i.e., >> 3.1-4)? >> >> You can also control the plotting dimensions manually. By >> default, the >> horizontal (x in a right or left-facing tree) is the total tree >> length + >> the label offset + the amount of space required to plot the tip >> labels; >> however this can be increased (or decreased) using the argument >> x.lim. >> This is also true of the phytools function plotTree, but in that >> case >> the analogous arguments are offset and xlim. >> >> My second problem: How can I locate the second set of >> symbols in the >> plot? >> For only one symbol-type, I used tiplabels(pch = , col = >> , cex = ). >> But if >> I woud like to put a second set of symbols, how should I >> put it next >> to the >> first set of the symbols? >> >> >> To get the x & y coordinates of a plotted tree created using >> plot.phylo >> or plotTree, we can steal from inside tiplabels: >> >> lastPP<-get("last_plot.phylo",__envir=.PlotPhyloEnv) >> >> x<-lastPP$xx[1:lastPP$Ntip] >> y<-lastPP$yy[1:lastPP$Ntip] >> >> Now, we can add points to our plot at coordinates x & y - and if >> we want >> to add two sets of points, we can offset the second set by >> adjusting >> slightly (for a right or left-facing tree) the x-coordinates. >> The order >> of x & y should be the order of bird.families$tip.label. >> >> _________________________________________________ >> >> 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 >> >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at >> http://www.mail-archive.com/r-__sig-phylo@r-project.org/ >> <http://www.mail-archive.com/r-sig-phylo@r-project.org/> >> >> >> >> >> -- >> *Pipoly Ivett* >> >> Ornithology Research Group >> University of Pannonia >> Tel.: +36 88 624249 >> Fax: +36 88 624747 >> pipoly.iv...@gmail.com <mailto:pipoly.iv...@gmail.com> >> +36 20 / 9236407 >> > -- *Pipoly Ivett* Ornithology Research Group University of Pannonia Tel.: +36 88 624249 Fax: +36 88 624747 pipoly.iv...@gmail.com +36 20 / 9236407 [[alternative HTML version deleted]]
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