Thanks a lot guys, for all the answers.
On the plot method of igraph, if i use rescale=F and i got the desired
effect. Below are my code with the desired effect.
I read the manual, but i think i did not notice the point, i think i got
used to xlim argument and this mislead me to the confusion, i'm sorry for
the confusion.
Anyway, thanks again for the patience, you helped me a lot.
Best wishes
Augusto Ribas
############################################################################
library(ape)
library(igraph)
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)
posicao<-matrix(c(rep(c(4,8),each=5),rep(1:5,2)),ncol=2,nrow=10)
plot(rtree(5),show.tip.label=F,use.edge.length = F,edge.width =
2,x.lim=c(0,10))
plot(dados.g,
layout=posicao,vertex.color=rep(c("green","yellow"),each=5),vertex.size=35,
vertex.label=NA,edge.color="black",edge.width=3,add=T,rescale=F)
axis(1)
axis(2)
##################################################################################
2014-03-19 18:50 GMT-04:00 Klaus Schliep <klaus.schl...@gmail.com>:
> 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
>>
>> [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> 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/
>>
>
>
>
> --
> Klaus Schliep
> Phylogenomics Lab at the University of Vigo, Spain
> http://darwin.uvigo.es/kschliep/
>
>
--
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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