[igraph] Question about ploting graph in animation

[Zhu, Hong]

Hello  igraph users,

I am trying to create animation and plot the network after each iteration. It 
does show the animation and change of the network.
But the problem is the graph does not have a fixed orientation, while on the 
contrast, the nodes move around over time with the
iterations.

I wonder whether there is something wrong with "layout" option. Because if we 
use "circle" or "tree" layout, the nodes are fixed but
it is not the graphical presentation we want.

Any comments to help? Thanks a lot in advance!

Best,

Hong 

The following is the code.

#
mrule <- function(A, y) {
# Majority rule dynamics
# A = adjacency matrix
# y = state of the vertices at time t
#
        apply(cbind(A, y), 1, z=y, function(x, z){
        n <- length(x)
        if (sum(x[-n]) == 0) return(x[n])
        z <- z[x[-n]==1]
        zf <- factor(z, levels=c(0,1))
        cz <- table(zf)
        if (cz[1] != cz[2]) c(0,1)[which.max(cz)] else rbinom(n=1, size=1, 
prob=0.5) 
        })
}


## nt is step, try nt=(25, 50, 100)
nt <- 50
ani.options(interval = 0.5, nmax = nt ,title="Animation for mrule")
ani.start()
par(mar=c(3,2.5,1,0.2),pch=20,mgp=c(1.5,0.5,0))
interval = ani.options("interval")

g1<-ba.game(100,m=2,directed=F)
g1<-add.edges(g1,c(97,98,98,99))
nv<-vcount(g1)
ne<-ecount(g1)
##Assign original status
y0<-V(g1)$status<-rbinom(nv, size=1, prob=0.5) # state of the nodes at time #= 0
V(g1)$color<-ifelse(V(g1)$status==0,"red","blue")

A <- get.adjacency(g1,binary=TRUE)
y_m<-y_p <- y0
s1_m <- rep(NA, nt)
s1_m[1] <- sum(y_m)
plot(g1,layout=layout.fruchterman.reingold, 
vertex.size=4,vertex.label=NA,edge.arrow.size=0.5)

for (i in 2:nt) {
        y_m <- mrule(A, y=y_m) # State at time = i - 1
        V(g1)$color<-ifelse(y_m==0,"red","blue")
        
plot(g1,layout=layout.fruchterman.reingold,vertex.size=4,vertex.label=NA,edge.arrow.size=0.5)
Sys.sleep(interval)
#dev.off()
}

_______________________________
Hong Zhu 
Ph.D. Candidate, Biostatistics 
Bloomberg School of Public Health 
Johns Hopkins University