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?
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
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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