[igraph] Re: Hello

[Walk to Sun]

Hi Dr Gábor Csárdi,

 

Thank you for your help.

 

The R function is supposed to be data varying widely in structure and content. Could you please help adjusting parameter so that beginners can learn Igraph grammar?

 

Best regards

W

 

 

1. The Fruchterman-Reingold layout algorithm

library(igraph)

library(Cairo)

source("frgraphs.R")

g <- read.graph("test.net",format="pajek")

graphs <- frgraphs()

lay <- lapply(graphs, layout.fruchterman.reingold, niter=3000)

 

CairoX11()

# CairoPNG(file="frplots.png")

par(mai=c(0,0,0,0))

layout(matrix(1:16, nr=4, byrow=TRUE))

layout.show(16)

for (i in seq(along=graphs)) {

  plot(graphs[[i]], layout=lay[[i]],

       vertex.label=NA, vertex.size=13, edge.color="black",

       vertex.color="red")

}

# dev.off()

 

 

 

 

2. The tkplot editor of the R package

cs <- leading.eigenvector.community.step(g)

V(g)$color <- ifelse(cs$membership==0, "lightblue", "green")

 

scale <- function(v, a, b) {

  v <- v-min(v) ; v <- v/max(v) ; v <- v * (b-a) ; v+a

}

 

V(g)$size <- scale(abs(cs$eigenvector), 10, 20)

E(g)$color <- "grey"

E(g)[ V(g)[ color=="lightblue" ] %--% V(g)[ color=="green" ] ]$color <- "red"

 

tkplot(g, layout=layout.kamada.kawai, vertex.label.font=2)

 

coords <- tkplot.getcoords(1)

 

 

3. Transparency with the Cairo R package

library(igraph) ; library(Cairo)

g <- barabasi.game(100, power=0.6, m=10)

V(g)$name <- seq(vcount(g))-1

g <- simplify(g)

l <- layout.fruchterman.reingold(g)

l <- layout.norm(l, -1,1, -1,1)

 

fcs <- fastgreedy.community(simplify(as.undirected(g)))

Q <- round(max(fcs$modularity), 3)

fcs <- community.to.membership(g, fcs$merges, steps=which.max(fcs$modularity)-1 )

 

CairoX11() # or CairoPNG(file="fastgreedy.png")

 

plot(g, layout=l, vertex.size=3, vertex.label=NA, vertex.color="#ff000033",

     vertex.frame.color="#ff000033", edge.color="#55555533", edge.arrow.size=0.3,

     rescale=FALSE, xlim=range(l[,1]), ylim=range(l[,2]),

     main=paste(sep="", "Fast greedy community detection,\nQ=", Q))

 

g2 <- subgraph(g, which(fcs$membership==fcs$membership[1])-1)

l2 <- l[ which(fcs$membership==fcs$membership[1]), ]

 

plot(g2, layout=l2, vertex.size=3, vertex.label=V(g2)$name,

     vertex.color="#ff0000", vertex.frame.color="#ff0000", edge.color="#555555",

     vertex.label.dist=0.5, vertex.label.cex=0.8, vertex.label.font=2,

     edge.arrow.size=0.3, add=TRUE, rescale=FALSE)

 

nodes <- which(fcs$membership==fcs$membership[1])-1

nodes <- paste(collapse=", ", nodes)

text(0,-1.3, nodes, col="blue")

 

# dev.off()

 

 

 

4. Plotting the diameter

library(igraph)

library(Cairo)

source("frgraphs.R")

g <- read.graph("test.net",format="pajek")

d <- get.diameter(g)

 

E(g)$color <- "grey"

E(g)$width <- 1

E(g, path=d)$color <- "red"

E(g, path=d)$width <- 2

V(g)$label.color <- "blue"

V(g)$color  <- "SkyBlue2"

V(g)[ d ]$label.color <- "black"

V(g)[ d ]$color <- "red"

 

plot(g, layout=layout.fruchterman.reingold,

     vertex.label.dist=0, vertex.size=15)

title(main="Diameter of the Zachary Karate Club network",

      xlab="created by igraph 0.4")

axis(1, labels=FALSE, tick=TRUE)

axis(2, labels=FALSE, tick=TRUE)

 

 

 

5. Degree distributions for nonlinear preferential attachment

library(igraph)

 

g <- barabasi.game(100000)

d <- degree(g, mode="in")

dd <- degree.distribution(g, mode="in", cumulative=TRUE)

alpha <- power.law.fit(d, xmin=20)

plot(dd, log="xy", xlab="degree", ylab="cumulative frequency",

     col=1, main="Nonlinear preferential attachment")

lines(10:500, 10*(10:500)^(-coef(alpha)+1))

 

powers <- c(0.9, 0.8, 0.7, 0.6)

for (p in seq(powers)) {

  g <- barabasi.game(100000, power=powers[p])

  dd <- degree.distribution(g, mode="in", cumulative=TRUE)

  points(dd, col=p+1, pch=p+1)

}

 

legend(1, 1e-5, c(1,powers), col=1:5, pch=1:5, ncol=1, yjust=0, lty=0)

 

 

 

6, Plotting the dendrogram of a community structure algorithm

library(igraph)

g <- read.graph("test.net",format="pajek")

wt <- walktrap.community(g, modularity=TRUE)

dend <- as.dendrogram(wt, use.modularity=TRUE)

plot(dend, nodePar=list(pch=c(NA, 20)))

 

 

 

7. Creating simple animations

library(igraph) ;library(Cairo)

g <- read.graph("test.net",format="pajek")

l <- layout.kamada.kawai(g, niter=1000)

ebc <- edge.betweenness.community(g)

 

colbar <- rainbow(6)

colbar2 <- c(rainbow(5), rep("black",15))

 

for (i in 1:20) {

 

  g2 <- delete.edges(g, ebc$removed.edges[seq(length=i-1)])

 

  eb <- edge.betweenness(g2)

  cl <- clusters(g2)$membership

  q <- modularity(g, cl)

 

  E(g2)$color <- "grey"

  E(g2)[ order(eb, decreasing=TRUE)[1:5]-1 ]$color <- colbar2[1:5]

 

  E(g2)$width <- 1

  E(g2)[ color != "grey" ]$width <- 2

 

  # CairoPNG(sprintf("eb-community-%04d.png", i))

  plot(g2, layout=l, vertex.size=6, vertex.label=NA,

       edge.label.color="red", vertex.color=colbar[cl+2],

       edge.label.font=2)

  title(main=paste("Q=", round(q,3)), font=2)

  ty <- seq(1,by=-strheight("1")*1.5, length=20)

  text(-1.3, ty, adj=c(0,0.5), round(sort(eb, dec=TRUE)[1:20],2), col=colbar2,

       font=2)

 

  # dev.off()

  scan()

}