library("igraph")
library("igraphdata")
library("network")
library("networkD3")
library("circlize")
library(sand)
set.seed(42)
g <- sample_gnp(50, 0.1, directed=FALSE)
edge_density(g) ##density of g
g.pa <- sample_pa(50, 1, directed=FALSE)
edge_density(g.pa) ##density of g
g
g.pa
data("aidsblog")
summary(aidsblog)
gm <- get.adjacency(g, sparse=F)
aidsm <- get.adjacency(aidsblog, sparse=F)
igraph.options(vertex.size=5, vertex.label=NA, vertex.color="orange", edge.size=15, edge.color="grey", edge.arrow.size=0.2)
par(mfrow=c(1, 3))
# random layout
plot(g, layout=layout_randomly)
# random layout
plot(g, layout=layout_randomly)
par(mfrow=c(1, 3))
# random layout
plot(g, layout=layout_randomly)
plot(g.pa, layout=layout_randomly)
title("random graph")
# random layout
plot(g, layout=layout_randomly)
title("random graph")
plot(g.pa, layout=layout_randomly)
title("pref. attachment")
plot(aidsblog, layout=layout_randomly)
title("Blog Network")
# random layout
plot(g, layout=layout_randomly)
# random layout
plot(g, layout=layout_randomly)
title("random graph")
plot(g.pa, layout=layout_randomly)
title("pref. attachment")
plot(aidsblog, layout=layout_randomly)
title("Blog Network")
#  circular layout
plot(g, layout=layout.circle)
title("random graph")
plot(g.pa, layout=layout.circle)
title("pref. attachment")
plot(aidsblog, layout=layout.circle)
title("Blog Network")
# Fruchterman & Reingold layout
plot(g, layout=layout_with_fr)
title("random graph")
title("random graph")
plot(g.pa, layout=layout_with_fr)
title("pref. attachment")
plot(aidsblog, layout=layout_with_fr)
title("Blog Network")
plot(g, layout=layout_with_mds)
title("random graph")
plot(g.pa, layout=layout_with_mds)
title("pref. attachment")
plot(aidsblog, layout=layout_with_mds)
title("Blog Network")
plot(g.pa, layout=layout_with_fr, vertex.label = V(g)$name)
V(g)$name
V(g)
g
V(g)$name
# MDS layout
plot(g, layout=layout_with_mds)
title("random graph")
plot(g.pa, layout=layout_with_mds)
title("pref. attachment")
plot(aidsblog, layout=layout_with_mds)
title("Blog Network")
plot(g, layout=layout_with_mds)
title("random graph")
plot(g.pa, layout=layout_with_mds)
title("pref. attachment")
plot(aidsblog, layout=layout_with_mds)
title("Blog Network")
# MDS layout
plot(g, layout=layout_with_mds)
# MDS layout
plot(g, layout=layout_with_mds)
plot(g, layout=layout_with_mds)
title("random graph")
plot(g.pa, layout=layout_with_mds)
title("pref. attachment")
plot(aidsblog, layout=layout_with_mds)
title("Blog Network")
plot(g, layout=layout_with_kk)
title("random graph")
plot(g.pa, layout=layout_with_kk)
title("pref. attachment")
plot(aidsblog, layout=layout_with_kk)
title("Blog Network")
dev.off()
distances(g, mode = "all")
distances(g.pa, mode = "all")
distances(aidsblog, mode = "all")
par(mar=c(0.5,0.5,0.5,0.5))
deg_g <- igraph::degree(g, mode = "all", normalized = T)
deg_g
deg_g*100
V(g)$size <- deg_g*100
V(g)$size
V(g)$name
V(g)$name <- 1:vcount(g)
V(g)$label.color <- "blue"
V(g)$name
plot(g, layout=layout_with_fr, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
title(main="Random graph. Node size = node degree centrality", cex.main=1)
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
clos_g <- igraph::closeness(g, mode = "all", normalized = T)
V(g)$size <- clos_g*30
V(g)$label.color <- "blue"
plot(g, layout=layout_with_fr, vertex.label = V(g)$name,  vertex.label.dist=0, vertex.label.cex=0.6)
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
V(g)$size <- betw_g*100
V(g)$label.color <- "blue"
plot(g, layout=layout_with_fr, layout=layout_with_fr, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
eigen_g <- eigen_centrality(g)
size
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
eigen_g <- eigen_centrality(g)
V(g)$size <- eigen_g$vector*10
V(g)$label.color <- "blue"
plot(g, layout=layout_with_fr, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
title(main="Random graph. Node size = node eigenvector centrality", cex.main=1)
?layout_with_fr
?layout_with_kk
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
plot(g.pa)
title(main="Graph layout default", cex.main=0.8)
plot(g.pa, layout=layout_randomly, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
title("Randomly place vertices _PA", cex.main=0.8)
plot(g.pa, layout=layout_with_fr, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
title(main="Fruchterman-Reingold layout -PA", cex.main=0.8)
plot(g.pa, layout=layout_with_kk, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
title(main="Kamada-Kawai layout -PA", cex.main=0.8)
plot(g.pa, layout=layout_in_circle, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
title(main="Graph layout circle -PA", cex.main=0.8)
plot(g.pa, layout=layout_with_mds, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
plot(g.pa, layout=layout_with_kk, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
plot(g.pa, layout=layout_with_mds, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
## Compute node degree and use it to set node size
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
deg_g.pa <- igraph::degree(g.pa, mode = "all", normalized = T)
V(g.pa)$name <-  1:vcount(g.pa)
V(g.pa)$label.color <- "blue"
V(g.pa)$size <- deg_g.pa*100
plot(g.pa, layout=layout_with_fr, vertex.label = V(g.pa)$name, vertex.label.dist=0, vertex.label.cex=0.6)
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
clos_g.pa <- closeness(g.pa, mode = "all", normalized = T)
V(g.pa)$size <- clos_g.pa*10
plot(g.pa, layout=layout_with_fr, vertex.label = V(g.pa)$name, vertex.label.dist=0, vertex.label.cex=0.6)
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
betw_g.pa <- betweenness(g.pa, directed = F, normalized = T)
V(g.pa)$size <- betw_g.pa*10
plot(g.pa, layout=layout_with_fr, vertex.label = V(g)$name, vertex.label.dist=0, vertex.label.cex=0.6)
title(main="Pref. Attach. graph. Node size = node betweenness centrality", cex.main=1)
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
eigen_g.pa <- eigen_centrality(g.pa)
V(g.pa)$size <- eigen_g.pa$vector*10
plot(g.pa, layout=layout_with_fr, vertex.label = V(g.pa)$name, vertex.label.dist=0, vertex.label.cex=0.6)
AB <- aidsblog
par(mfrow=c(2,3))
plot(AB)
title(main="Graph layout default", cex.main=0.8)
plot(AB, layout=layout_randomly)
title("Randomly place vertices _AB", cex.main=0.8)
plot(AB, layout=layout_with_fr)
title(main="Fruchterman-Reingold layout -AB", cex.main=0.8)
plot(AB, layout=layout_with_kk)
title(main="Kamada-Kawai layout -AB", cex.main=0.8)
plot(AB, layout=layout_in_circle)
title(main="Graph layout circle -AB", cex.main=0.8)
plot(AB, layout=layout_with_mds)
title(main="Graph layout multidimensional scaling -AB", cex.main=0.8)
dev.off()
coord <-  layout_with_fr(AB)
coord
coord <-  layout_with_fr(AB)
## Compute node indegree and use it to set node size
par(mar=c(0.5,0.5,0.5,0.5)) ### set margins
indeg_AB<- igraph::degree(AB, mode = "in", normalized = T)
plot(AB, layout=coord, vertex.size=V(AB)$Indegsize)
title(main="Aidsblog. Node size = node indegree centrality", cex.main=1)
palf <- colorRampPalette(c("white", "red"))
heatmap(flom[, 16:1], Rowv = NA, Colv = NA, col = palf(2),
scale="none", margins=c(6,6) )