[R-sig-eco] combine 2 plots - one network and one phylogenetic tree
Augusto Ribas
ribas.aca at gmail.com
Wed Jun 20 17:07:15 CEST 2012
What i want is something like:
#Take the order of the hosts from the tree
order<-host.tree$tip.lab
par(mfrow=c(2,1))
#remove the host names from the tree to not repeat the network
plot(host.tree,use.edge.length=F,direction="downwards",show.tip.label =F)
#now plot the network, with the order of the tree
plotweb(dados[,order],method = "normal")
#but cant make the H2 label of the tree in the exactly place of the
#H2 of the network, and for all the Host species.
#I dont know a strategy to make a plot this way.
#The distance from H1 to H2 to H3 are variable in the network plot, i
#would like someway to make them be equall, then maybe i could work the
#mar parameter in par to make things plug right, i dont know.
#something like this draw:
http://oi47.tinypic.com/2j2szcy.jpg
2012/6/20 Alan Haynes <aghaynes at gmail.com>:
> Sorry, for the multiple posting.
>
> Assuming you want what I think you want, you actually have everything in
> your code, just in the wrong order and with the mfrow argument reversed:
>
>
> library(igraph)
> dados.network<-cbind(expand.grid(rownames(dados),colnames(dados)),Presence=c(dados[,]))
> dados.network<-dados.network[which(dados.network$Presence==1),1:2]
> dados.igraph<-graph.data.frame(dados.network)
>
>
> library(ape)
>
> host.tree<-rtree(6,rooted=TRUE,tip.label=paste("H",1:6,sep=""))
>
> par(mfrow=c(1,2))
>
> 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="")))
> plot(host.tree,use.edge.length=F,direction="right")
>
>
>
> If you particularly want the graphic in portrait then you use tiff or jpeg
> functions to generate a tall, narrow figure. Something like this
>
> tiff("filename.tiff", width=3, height = 6, units="in", res=600)
>
> par(mfrow=c(2,1))
>
> 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="")))
> plot(host.tree,use.edge.length=F,direction="right")
>
> dev.off()
>
>
> Does that solve it?
>
>
>
> Alan
>
>
> --------------------------------------------------
> Email: aghaynes at gmail.com
> Mobile: +41794385586
> Skype: aghaynes
>
>
> On 20 June 2012 16:23, Charles Novaes de Santana <charles.santana at gmail.com>
> wrote:
>>
>> 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
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
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>
>
--
Grato
Augusto C. A. Ribas
Site Pessoal: http://augustoribas.heliohost.org
Lattes: http://lattes.cnpq.br/7355685961127056
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