Dear Augusto,
below are some comments about plot.phyo.
Tchau
Klaus
On Wed, Mar 19, 2014 at 10:35 PM, Augusto Ribas <ribas....@gmail.com> wrote:
> Hello.
>
> I'm trying to combine 2 plots, a phylogeny and a network.
> but i'm having a little problems.
>
> i have two question about the phylogeny plot and one about igraph, but
> about igraph i'll look for help on the package forum too, so no worries,
> but in case someone know igraph, the question is here too.
> The code for the figures i refer are in the end of the message.
>
>
> About plot.phylo.
>
> Question 01.
> Look at figure 1, the tree are plotted and every tip have their coordinates
> in X and Y axis, i would like to know how to extract them, for example, tip
> 1 end at x=4 and y=1, tip 2 end at x=4, y=2, are there a way to easy
> extract that directly, to use for others purposes, like add others things
> to the plot?
This is probably all you need:
set.seed(15)
tree = rtree(5)
plotdata <- plot(tree,show.tip.label=F,use.edge.length = F,edge.width = 2)
plotinfo <- get("last_plot.phylo", envir = .PlotPhyloEnv)
plotdata
plotinfo
points(plotinfo$xx, plotinfo$yy)
nodelabels()
tiplabels()
> Question 02
> How do i control the x limits, for example, figure 1, the tree, i would
> like the x axis to begin in 0 and end in 15 for example, The tree occupy
> the 0 to 4 length in x axis, i would like to have empty space to put things
> (particularly a network with my parameters), so i just want some more space
> in the figure, i don't know how to control it or if i'm allowed to do so
> for this function.
>
> I tryed to use xlim=c(0,15)
>
> > plot(rtree(5),show.tip.label=F,use.edge.length = F,edge.width =
> 2,xlim=c(0,15))
> Erro em plot.default(0, type = "n", xlim = x.lim, ylim = y.lim, xlab = "",
> :
> argumento formal "xlim" corresponde a múltiplos argumentos especificados
>
> The argument for plot.phylo is called x.lim not xlim, reading the manual
sometimes helps ;) So this works:
plot(rtree(5),show.tip.label=F,use.edge.length = F,edge.width =2,
x.lim=c(0,15))
> But my guess is that the function already use it (the xlim argument), so i
> could not change it like this.
> Use par(mfrow=c(1,2)) or the layout() function do not allow me to glue
> perfectly the network and the tree, so how do i leave empty space to add
> things?
>
> Question 03. (no worries here, but just in case)
> The igraph plot function centralize the coordinates in and limits the plot
> between 1 and -1, both for x and y axis, how do i disable this feature, for
> example, when i create the matrix posicao with the positions that i desire
> for the vertices(nodes), when i say vertice 1 to be at x=1 and y=1, it
> really be there, and now be recalculated to stay between -1 and 1.
>
>
>
>
> Sample code
>
> #packages
> library(ape)
> library(igraph)
>
>
> #generate some data
> set.seed(15)
> pol.s<-paste("Polinizador",1:5)
> flor.s<-paste("Flor",1:5)
>
> dados<-data.frame(pol=sample(pol.s,15,replace=T),flor=sample(flor.s,15,replace=T))
>
> dados.g <-graph.data.frame(unique(dados), directed=F)
>
> #position matrix, each line is the position of a vertice(node)
> posicao<-matrix(c(rep(1:2,each=5),rep(1:5,2)),ncol=2,nrow=10)
>
>
> #Figure 1
> plot(rtree(5),show.tip.label=F,use.edge.length = F,edge.width = 2)
> axis(1)
> axis(2)
>
> #figure 2
> plot(dados.g,
> layout=posicao+1,vertex.color=rep(c("green","yellow"),each=5),
> vertex.shape=rep(c("square","circle"),each=5),vertex.size=35,
> vertex.label=c(paste("Pol",1:5),paste("Flor",1:5)),edge.color="black",
> edge.width=3)
> axis(1)
> axis(2)
>
>
> #figure 3
> #i would like to glues these two guys, but i need to better control the
> arguments
> #and i dont know how :(
> plot(rtree(5),show.tip.label=F,use.edge.length = F,edge.width = 2)
> par(new=T)
> plot(dados.g, layout=posicao,vertex.color=rep(c("green","yellow"),each=5),
> vertex.shape=rep(c("square","circle"),each=5),vertex.size=35,
> vertex.label=c(paste("Pol",1:5),paste("Flor",1:5)),edge.color="black",
> edge.width=3,add=T)
>
> --
> Grato
> Augusto C. A. Ribas
>
> Site Pessoal: http://recologia.com.br/ <http://augustoribas.heliohost.org>
> Github: https://github.com/Squiercg
> Lattes: http://lattes.cnpq.br/7355685961127056
>
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>
>
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>
--
Klaus Schliep
Phylogenomics Lab at the University of Vigo, Spain
http://darwin.uvigo.es/kschliep/
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