Code Rnet 1

% HSE example 1; December 4, 2018
*vertices 6
1 a
2 f
3 c
4 b
5 d
6 e
*arcs
1 4
2 6
3 2
4 5
     5       1
6 3
*edges
1 5
3 4
3 3

Our network HSEexample1.net has no coordinates data. Pajek puts nodes on the circle:

ex1circ.svg

We changed some weights and computed the alldegree vector and indegree partition. We used them in the visualization. After some changes of graphical options we get:

ex1.eps ex1.pdf ex1.svg

Using Inkscape we enhanced the obtained SVG picture: changing a label, improving the shape and position of a loop, changing the position of parallel links, adding text, adding region, …

ex1ink.svg ex1ink.pdf

We saved the network as a Pajek project file HSEexample1.paj and the graphical settings on the file HSEexample1.ini.

Collection 2015

C:\Users\batagelj\Documents\papers\2017\Moscow\Rnet\test\nets

• tinaSet - visualization, criteria
• class
• SaKtrade - matrix permutation
• USAair - ZOOM
• mreza
• GR30_60 - 3D

> setwd("C:/Users/batagelj/Documents/papers/2018/moskva/december/nets")
> library(igraph)
> links <- c("A","C", "A","G",
+   "B","C", "B","A", "B","E",
+   "C","A", "C","E", "D","B", 
+   "D","G", "D","E", "E","A",
+   "F","E", "G","C", "G","F")
> L <- graph(links)
> L
IGRAPH bb7e45b DN-- 7 14 -- 
+ attr: name (v/c)
+ edges from bb7e45b (vertex names):
 [1] A->C A->G B->C B->A B->E C->A C->E D->B D->G D->E E->A F->E G->C G->F
> plot(L)
> vcount(L)
[1] 7
> ecount(L)
[1] 14
> L <- L + vertex("H")
> plot(L)

> V(L)
+ 8/8 vertices, named, from 84e744b:
[1] A C G B E D F H
> E(L)
+ 14/14 edges from 84e744b (vertex names):
 [1] A->C A->G B->C B->A B->E C->A C->E D->B D->G D->E E->A F->E G->C G->F
> V(L)$name
[1] "A" "C" "G" "B" "E" "D" "F" "H"
> V(L)$name[5] <- "John"
> V(L)$color <- sample(c("yellow","cyan"),vcount(L),rep=TRUE)
> plot(L)
> ye <- V(L)[color=="yellow"]; cy <- V(L)[color=="cyan"]
> E(L)[ye %--% cy]$color <- "red"
> E(L)[ye %--% ye]$color <- "blue"
> E(L)[cy %--% cy]$color <- "blue"
> L$name <- "Example"
> E(L)$weight <- sample(1:10,ecount(L),rep=TRUE)
> graph_attr_names(L)
[1] "name"
> graph_attr(L)
$name
[1] "Example"
> vertex_attr_names(L)
[1] "name"  "color"
> edge_attr_names(L)
[1] "color"  "weight"
> w <- E(L)$weight;  plot(L,edge.width=w)
> write.graph(L,"Links.net",format="pajek")
> L
IGRAPH b8d9e7d DNW- 8 14 -- Example
+ attr: name (g/c), name (v/c), color (v/c), color (e/c), weight (e/n)
+ edges from b8d9e7d (vertex names):
 [1] A   ->C    A   ->G    B   ->C    B   ->A    B   ->John C   ->A    C   ->John
 [8] D   ->B    D   ->G    D   ->John John->A    F   ->John G   ->C    G   ->F   
> 

> library(igraphdata)
> data(package="igraphdata")
> data(UKfaculty) 
> ?UKfaculty
> UKfaculty
IGRAPH 6f42903 D-W- 81 817 -- 
+ attr: Type (g/c), Date (g/c), Citation (g/c), Author (g/c), Group (v/n),
| weight (e/n)
+ edges from 6f42903:
 [1] 57->52 76->42 12->69 43->34 28->47 58->51  7->29 40->71  5->37 48->55  6->58 21-> 8
[13] 28->69 43->21 67->58 65->42  5->67 52->75 37->64  4->36 12->49 19->46 37-> 9 74->36
[25] 62-> 1 15-> 2 72->49 46->62  2->29 40->12 22->29 71->69  4-> 3 37->69  5-> 6 77->13
[37] 23->49 52->35 20->14 62->70 34->35 76->72  7->42 37->42 51->80 38->45 62->64 36->53
[49] 62->77 17->61  7->68 46->29 44->53 18->58 12->16 72->42 52->32 58->21 38->17 15->51
[61] 22-> 7 22->69  5->13 29-> 2 77->12 37->35 18->46 10->71 22->47 20->19 19->31 68->13
[73] 49->69 30->63  5->49 53->75 62->57 73->81 29->69 71->40 19->58 49->42 37-> 5 18-> 2
+ ... omitted several edges
> 

Data sets in package igraphdata:

igraph's write.graph function produces incorrect Pajek's net file:

• color names are not compatible with Pajek's names; they are exported in quotes ” ;
• node labels are not exported

Here is a partial solution igraph+.R for exporting network as a Pajek project file:

empty <- character(0)

normalize <- function(x,marg=0) return ((1-2*marg)*(x-min(x))/(max(x)-min(x))+marg)

write.graph.paj <- function(N,file="test.paj",vname="name",coor=NULL,va=NULL,ea=NULL,
  weight="weight",ecolor="color"){
  n <- gorder(N); m <- gsize(N); ga <- graph_attr_names(N)
  if(is.null(va)) va <- vertex_attr_names(N)
  if(is.null(ea)) ea <- edge_attr_names(N)
  va <- union(va,vname); ea <- union(ea,weight)
  paj <- file(file,"w")
  cat("*network",file,"\n",file=paj)
  cat("% saved from igraph ",format(Sys.time(), "%a %b %d %X %Y"),"\n",sep="",file=paj)
  for(a in ga) cat("% ",a,": ",graph_attr(N,a),"\n",sep="",file=paj)
  cat('*vertices ',n,'\n',file=paj)
  lab <- if(vname %in% va) vertex_attr(N,vname) else paste("v",1:n,sep="") 
  if(is.null(coor)){  
    if(vname %in% va) for(v in V(N)) cat(v,' "',lab[v],'"\n',sep="",file=paj)
  } else { 
    for(v in V(N)) cat(v,' "',lab[v],'" ',paste(coor[v,],collapse=" "),'\n',sep="",file=paj) 
  }
  va <- setdiff(va,vname)
  cat(ifelse(is_directed(N),"*arcs\n","*edges\n"),file=paj)
  K <- ends(N,E(N),names=FALSE) 
  w <- if(weight %in% ea) edge_attr(N,weight) else rep(1,m)
  if(ecolor %in% ea){ C <- edge_attr(N,ecolor)
    for(e in 1:m) cat(K[e,1]," ",K[e,2]," ",w[e]," c ",as.character(C[e]),"\n",sep="",file=paj)
  } else 
    for(e in 1:m) cat(K[e,1]," ",K[e,2]," ",w[e],"\n",sep="",file=paj)
  ea <- setdiff(ea,c(weight,ecolor)); nr <- 1
  for(a in ea){nr <- nr+1; w <- edge_attr(N,a)
    cat(ifelse(is_directed(N),"*arcs","*edges"),file=paj)
    cat(" :",nr,' "',a,'"\n',sep="",file=paj)
    if(is.numeric(w)){
      for(e in 1:m) cat(K[e,1]," ",K[e,2]," ",w[e],"\n",sep="",file=paj)
    } else if(is.character(w)){ 
      W <- factor(w); lev <- levels(W)
      for(i in seq_along(lev)) cat("%",i,"-",lev[i],"\n",file=paj)
      for(e in 1:m) cat(K[e,1]," ",K[e,2]," ",W[e],' l "',w[e],'"\n',sep="",file=paj)
    } else warning(paste("unsupported type of",a),call.=FALSE)
  }
  cat("\n",file=paj)
  for(a in va){
    S <- vertex_attr(N,a); ok <- TRUE
    if(is.character(S)){
      cat("*partition ",a,"\n",sep="",file=paj)
      s <- factor(S); lev <- levels(s)
      for(i in seq_along(lev)) cat("%",i,"-",lev[i],"\n",file=paj)
    } else if(is.numeric(S)){ 
      s <- S; cat("*vector ",a,"\n",sep="",file=paj) 
    } else {warning(paste("unsupported type of",a),call.=FALSE); ok <- FALSE}
    if(ok){cat('*vertices ',n,'\n',file=paj)
      for(v in 1:n) cat(s[v],"\n",file=paj)
      cat("\n",file=paj) }
  }
  close(paj)
}

Additional options should be included and some temporary quantities eliminated.

> source("https://raw.githubusercontent.com/bavla/Rnet/master/R/igraph+.R")
# source("./igraph+.R")
> P <- tkplot(L,500,500,edge.curved=0.25,edge.width=w)
> coor <- tkplot.getcoords(P,norm=F)
> xy <- cbind(normalize(coor[,1],marg=0.05),normalize(coor[,2],marg=0.05))
> source("./igraphEx.R")
> write.graph.paj(L,"networkB.paj",coor=xy)

> source("./igraph+.R")
> data(USairports)
> ?USairports 
> USairports
> write.graph.paj(USairports,"USairports.paj",weight="Departures",va=empty,ea=empty)
> write.graph.paj(USairports,"USairports2.paj",weight="Departures",vname="City",va="City",ea=c("Seats","Passengers"))

Suppose that a sequence S = s₁, s₂, s₃, …, s_k-1, s_k is given. It determines a directed “summary” network N = (V,A) where the set of nodes V is the set of all different elements (values) in S, and the set (list) of arcs A consists of all pairs (s_i, s_i+1), i = 1, …, k-1.

For an example we will take for a sequence the letters from a given text. The network construction can be applied to any sequence (pages on the web site visited by a user, attractions in a city or region visited by a tourist, …).

> setwd("C:/Users/batagelj/Documents/papers/2018/moskva/december/nets")
> s <- "we changed some weights and computed the alldegree vector and indegree partition"
> k <- nchar(s)
> S <- substring(s,1:k,1:k)
> F <- factor(S)
> V <- levels(F); n <- length(V)
> from <- as.integer(factor(S[1:(k-1)],levels=V))
> to <- as.integer(factor(S[2:k],levels=V))
> net <- file("seq.net","w"); cat('*vertices ',n,'\n',file=net)
> for(v in 1:n) cat(v,' "',V[v],'"\n',sep='',file=net)
> cat('*arcs\n',file=net)
> for(a in 1:(k-1)) cat(from[a],' ',to[a],'\n',sep='',file=net)
> close(net)

> setwd("C:/Users/batagelj/Documents/papers/2018/moskva/december/nets")
> library(igraph)
> source("https://raw.githubusercontent.com/bavla/Rnet/master/R/igraph+.R")
> s <- "we changed some weights and computed the alldegree vector and indegree partition"
> k <- nchar(s)
> S <- substring(s,1:k,1:k)
> G <- make_directed_graph(rbind(S[1:(k-1)],S[2:k]))
> graph_attr(G)$name <- s
> G
IGRAPH c07d9bb DN-- 19 79 -- we changed some weights and computed the alldegree vector an
+ attr: name (g/c), name (v/c)
+ edges from c07d9bb (vertex names):
 [1] w->e e->   ->c c->h h->a a->n n->g g->e e->d d->   ->s s->o o->m m->e e->   ->w w->e
[18] e->i i->g g->h h->t t->s s->   ->a a->n n->d d->   ->c c->o o->m m->p p->u u->t t->e
[35] e->d d->   ->t t->h h->e e->   ->a a->l l->l l->d d->e e->g g->r r->e e->e e->   ->v
[52] v->e e->c c->t t->o o->r r->   ->a a->n n->d d->   ->i i->n n->d d->e e->g g->r r->e
[69] e->e e->   ->p p->a a->r r->t t->i i->t t->i i->o o->n
> write.graph.paj(G,"seqi.paj")

Data at Github.

# setwd("C:/Users/batagelj/work/Python/graph/SVG/EUSN")
# colC <- c(rep("character",4),rep("numeric",7)); nas=c("","NA","NaN")
colC <- c(rep("character",4),rep("numeric",5)); nas=c("","NA","NaN")
nodes <- read.csv2("bibNodes.csv",encoding='UTF-8',colClasses=colC,na.strings=nas)
n <- nrow(nodes); M <- factor(nodes$mode); S <- factor(nodes$sex)
mod <- levels(M); sx <- levels(S); S <- as.numeric(S); S[is.na(S)] <- 0
links <- read.csv2("bibLinks.csv",encoding='UTF-8',colClasses="character")
F <- factor(links$from,levels=nodes$name,ordered=TRUE)
T <- factor(links$to,levels=nodes$name,ordered=TRUE)
R <- factor(links$relation); rel <- levels(R)
net <- file("bib.net","w"); cat('*vertices ',n,'\n',file=net)
clu <- file("bibMode.clu","w"); sex <- file("bibSex.clu","w")
cat('%',file=clu); cat('%',file=sex)
for(i in 1:length(mod)) cat(' ',i,mod[i],file=clu)
cat('\n*vertices ',n,'\n',file=clu)
for(i in 1:length(sx)) cat(' ',i,sx[i],file=sex)
cat('\n*vertices ',n,'\n',file=sex)
for(v in 1:n) {
  cat(v,' "',nodes$name[v],'"\n',sep='',file=net);
  cat(M[v],'\n',file=clu); cat(S[v],'\n',file=sex)
}
for(r in 1:length(rel)) cat('*arcs :',r,' "',rel[r],'"\n',sep='',file=net)
cat('*arcs\n',file=net)
for(a in 1:nrow(links))
  cat(R[a],': ',F[a],' ',T[a],' 1 l "',rel[R[a]],'"\n',sep='',file=net)
close(net); close(clu); close(sex)

To do: add node attributes and link attributes

# export igraph network in netSON basic format
# by Vladimir Batagelj, December 2018
# based on transforming CSV files to JSON file, by Vladimir Batagelj, June 2016 
# setwd("C:/Users/batagelj/Documents/papers/2018/moskva/december/nets")
library(igraph)
library(rjson)

write.graph.netJSON <- function(N,file="test.json",vname="name" ){
  n <- gorder(N); m <- gsize(N); dir <- is_directed(N)
  lType <- ifelse(dir,"arc","edge")
  va <- vertex_attr_names(N); ea <- edge_attr_names(N)
  vlab <- if(vname %in% va) vertex_attr(N,vname) else paste("v",1:n,sep="")
  va <- setdiff(va,vname)  
  nods <- vector('list',n); lnks <- vector('list',m)
  today <- format(Sys.time(), "%a %b %d %X %Y")
  for(i in 1:n) { L <- list(id=i,name=vlab[i]) 
    for(a in va) L[[a]] <- vertex_attr(N,a)[i]
    nods[[i]] <- L }
  for(i in 1:m) {uv <- ends(N,i,names=FALSE); u <- uv[1]; v <- uv[2]
    L <- list(id=i,type=lType,n1=u,n2=v)
    for(a in ea) L[[a]] <- edge_attr(N,a)[i]
    lnks[[i]] <- L }
  meta <- list(date=today,title="saved from igraph")
  leg <- list(mode="mod",sex="sx",rel="rel")
  inf <- graph_attr(N)
  if("name" %in% names(inf)) {inf["title"] <- inf$name; inf[["name"]] <- NULL}
  inf["network"] <- "bib"; inf["org"] <- 1
  inf["nNodes"] <- n; 
  if(dir) {inf["nArcs"] <- m; inf["nEdges"] <- 0} else {inf["nArcs"] <- 0; inf["nEdges"] <- m}
  inf[["legend"]] <- leg; 
  if("meta" %in% names(inf)) { k <- length(inf[["meta"]]); inf[["meta"]][[k+1]] <- meta
  } else inf[["meta"]] <- meta
  data <- list(netJSON="basic",info=inf,nodes=nods,links=lnks)
  json <- file(file,"w"); cat(toJSON(data),file=json); close(json)
}

> setwd("C:/Users/batagelj/Documents/papers/2018/moskva/december/nets")
> library(igraph)
> library(igraphdata)
> data(package="igraphdata")
> data(karate)
> library(igraph+)
> write.graph.netJSON(karate,file="karate.json")

Rnet