[R-sig-eco] combine 2 plots - one network and one phylogenetic tree

[Charles Novaes de Santana]

Hi Augusto,

Which layout do you want to reproduce? The layout of the first network
you plot?

Do you know the "tkplot" function of igraph? You can plot the network
using tkplot and then you can read the coordinates of the nodes into a
variable. Like this:

tkplot(dados.igraph,layout=layout.fruchterman.reingold,vertex.color=c(rep("red",6),rep("green",6)),edge.arrow.size=0.2,vertex.size=20,vertex.label=c(paste("P",1:6,sep=""),paste("H",1:6,sep="")));
my_layout<-tkplot.getcoords(1);

So you can use the variable my_layout (a matrix of coordinates) in
other plots of network you want to:

plot(dados.igraph, layout=my_layout)

Sorry if it is not what you are looking for. Maybe if you write
directly to the igraph-help mailing list you can have more luck. They
use to answer the questions quickly:

https://groups.google.com/forum/?fromgroups#!forum/network-analysis-with-igraph

All the best,

Charles

On Wed, Jun 20, 2012 at 4:04 PM, Augusto Ribas <ribas.aca at gmail.com> wrote:
> Hello.
> I was using the package ipgraph to plot networks of parasites and hosts.
> Then i though about plug a phylogeny tree on the plot. But I'm having some
> difficulties to do so.
>
> I'll give and CMR , hope someone can help.
>
> #I have data that look like this, 6 parasites ("P") and six host species
> ("P")
> dados<-matrix(c(1,1,1,1,0,0,
>                0,1,1,1,0,0,
>                0,0,1,1,0,0,
>                0,0,0,0,1,0,
>                0,0,0,0,0,1,
>                0,0,0,0,0,1),byrow=T,ncol=6,nrow=6,
>                dimnames=list(paste("P",1:6,sep=""),paste("H",1:6,sep="")))
> dados
>
> #Then i convert the data a way i can use with igraph packages
> #Is there a more elegant way to change data like this anyway?
>
> library(igraph)
> dados.network<-cbind(expand.grid(rownames(dados),colnames(dados)),Presence=c(dados[,]))
> dados.network<-dados.network[which(dados.network$Presence==1),1:2]
> dados.igraph<-graph.data.frame(dados.network)
>
> plot(dados.igraph,layout=layout.fruchterman.reingold,
> vertex.color=c(rep("red",6),rep("green",6)),edge.arrow.size=0.2,vertex.size=20,
> vertex.label=c(paste("P",1:6,sep=""),paste("H",1:6,sep="")))
>
> #now i would like to combine 2 plots,
> #one phylogenetic tree of the hosts:
>
> library(ape)
> host.tree<-rtree(6,rooted=TRUE,tip.label=paste("H",1:6,sep=""))
>
> #with the netwrok, but the network would have to had  a layout like in
> package bipartite
> library(bipartite)
>
> #something like this
> par(mfrow=c(2,1))
> plot(host.tree,use.edge.length=F,direction="downwards")
> plotweb(dados)
>
>
> Althoguht plotweb() do what i would like, in a pretty beautiful graph, i
> could not make it do equidistant representation  for the host species, nor
> reproduce this layout with igraph.
> If i could reproduce the layout on plot.igraph(), i think it would be easy
> to plug the tree on the network.
> So anyone know if there is an easy way to do what i'm trying? I'm pretty
> stuck here
>
> Thanks for your attention.
>
> Best wishes
> Augusto Ribas
>
>
> --
> Grato
> Augusto C. A. Ribas
>
> Site Pessoal: http://augustoribas.heliohost.org
> Lattes: http://lattes.cnpq.br/7355685961127056
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology



-- 
Um axé! :)

--
Charles Novaes de Santana
http://www.imedea.uib-csic.es/~charles
PhD student - Global Change
Laboratorio Internacional de Cambio Global
Department of Global Change Research
Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
Calle Miquel Marques 21, 07190
Esporles - Islas Baleares - España

Office phone - +34 971 610 896
Cell phone - +34 660 207 940