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>:
> 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/
>> email: 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.
>>
>> _______________________________________________
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>> Searchable archive at
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>>
>>
--
*Pipoly Ivett*
Ornithology Research Group
University of Pannonia
Tel.: +36 88 624249
Fax: +36 88 624747
pipoly.iv...@gmail.com
+36 20 / 9236407
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