network analysis

Plot Network Data in R with iGraph

/ willchernoff / Leave a comment

I recently had a conversation on Twitter about a plot I made a while back. Recall, the plot showed my Twitter network, my friends and my friend’s friends.

Here’s the Twitter thread:

And here’s the R code:

#### Load R libraries
library("iGraph")

#### Load edgelist
r <- read.csv(file="edgelist_friends.csv-03-25.csv",header=TRUE,stringsAsFactors=FALSE)[,-1]

#### Convert to graph object
gr <- graph.data.frame(r,directed=TRUE)

#### gr
# Describe graph
summary(gr)
ecount(gr) # Edge count
vcount(gr) # Node count
diameter(gr) # Network diameter
farthest.nodes(gr) # Nodes furthest apart
V(gr)$indegree = degree(gr,mode="in") # Calculate indegree

#### Plot graph
E(gr)$color = "gray"
E(gr)$width = .5
E(gr)$arrow.width = .25
V(gr)$label.color = "black"
V(gr)$color = "dodgerblue"
V(gr)$size = 4

set.seed(40134541)
l <- layout.fruchterman.reingold(gr)

pdf("network_friends_plot.pdf")
plot(gr,layout=l,rescale=TRUE,axes=FALSE,ylim=c(-1,1),asp=0,vertex.label=NA)
dev.off()
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Plot and Highlight All Clique Triads in VISONE

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snaCliques

Description

This post describes how to identify group structures among a network of respondents in VISONE. For a network of selections we identify any cliques involving three or more members. A clique is defined as a group containing three or more members where everyone has chosen everyone else.

Identify all triads

A tried is a network structure containing exactly three members. There are many types of triads. A group of three members where everyone chooses everyone else is a triad (i.e., a clique). A group of three members where two people choose each other and nobody choose the third member is another type of triad. There are 16 unique ways three people can select each other.

Identify all triads. Click the ‘analysis’ tab. Next to ‘task’, select ‘grouping’ from the drop down list of available options. Select ‘cohesiveness’ from the drop down list next to ‘class’. Select the option ‘triad census’ next to ‘measure’. Click ‘analyze’.

Highlight all cliques

Highlight all cliques. Click an empty part of the graph. Press the keys ‘Ctrl’ and ‘a’. Open the attribute manager. Click the ‘link’ button. Click the ‘filter’ button. Select ‘default value’ from the first drop down list. Select ‘triadType300’ from the second drop down list. Select ‘has individual value’ from the third drop down list. Click the radial button ‘replace’. Click ‘select’. Click ‘close’.

From the main VISONE drop down bar, select ‘links’. Click ‘properties’. Click the given color next to ‘color:’. Select ‘rgb’ tab. Set the ‘red’, ‘green’, and ‘blue’ values to 0. Set the ‘alpha’ value to 255. Set ‘opacity’ to 50%. Click the ‘close’ button. Set the ‘width:’ value to 5.0. From the ‘edge properties’ dialogue box, click the ‘apply’ button. Click ‘close.

Reduce visibility of all non-clique selections. Select all nodes and links. Click an empty part of the graph. Press the keys ‘Ctrl’ and ‘a’. Open the attribute manager. Click the ‘link’ button. Click the ‘filter’ button. Select ‘default value’ from the first drop down list. Select ‘triadType300’ from the second drop down list. Select ‘has individual value’ from the third drop down list. Click the radial button ‘remove’. Click ‘select’. Click ‘close’.

From the main VISONE drop down bar, select ‘links’. Click ‘properties’. Click the given color next to ‘color:’. Set ‘opacity’ to 20%. Set the ‘width:’ value to 2.0. From the ‘edge properties’ dialogue box, click the ‘apply’ button. Click ‘close.

How to plot a network subgraph on a network graph using R

/ willchernoff / 6 Comments

plotSubgraphOnGraph
Here is an example of how to highlight the members of a subgraph on a plot of a network graph.

## Load R libraries
library(igraph)

# Set adjacency matrix
g <- matrix(c(0,1,1,1, 1,0,1,0, 1,1,0,1, 0,0,1,0),nrow=4,ncol=4,byrow=TRUE)

# Set adjacency matrix to graph object
g <- graph.adjacency(g,mode="directed")

# Add node attribute label and name values
V(g)$name <- c("n1","n2","n3","n4")

# Set subgraph members
c <- c("n1","n2","n3")

# Add edge attribute id values
E(g)$id <- seq(ecount(g))

# Extract supgraph
ccsg <- induced.subgraph(graph=g,vids=c)

# Extract edge attribute id values of subgraph
ccsgId <- E(ccsg)$id

# Set graph and subgraph edge and node colors and sizes
E(g)$color="grey"
E(g)$width=2
E(g)$arrow.size=1
E(g)$arrow.width=1
E(g)[ccsgId]$color <- "#DC143C" # Crimson
E(g)[ccsgId]$width <- 2
V(g)$size <- 4
V(g)$color="#00FFFF" # Cyan
V(g)$label.color="#00FFFF" # Cyan
V(g)$label.cex <-1.5
V(g)[c]$label.color <- "#DC143C" # Crimson
V(g)[c]$color <- "#DC143C" # Crimson

# Set seed value
set.seed(40041)

# Set layout options
l <- layout.fruchterman.reingold(g)

# Plot graph and subgraph
plot.igraph(x=g,layout=l)

Simple, no?

Import *.csv Adjacency Matrix with Row and Column Names into R

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Here is some quick and dirty code for entering an adjacency matrix into R. These data were originally manipulated in Excel 2010 and saved as a comma delimitated *.csv file. The original file had sorted actor names down the first column and the same names along the first row. No value was present in the upper lefthand cell of the original data matrix.

# Load network data
# Expected format: adjacency matrix with corresponding row and column names
# Expected file type: *.csv
year1<-read.csv("networkData.csv",header=FALSE,stringsAsFactors=FALSE,sep=",")
rNames<-year1[-1,1]                                   # Get row names
cNames<-as.vector(as.character(year1[1,-1]))          # Get column names
year1<-apply(as.matrix(year1[-1,-1]),2,as.numeric)    # Get network matrix
year1[is.na(year1)]<-0                                # Set missing ties to 0
row.names(year1)<-rNames                              # Give row names
colnames(year1)<-cNames                               # Give column names

CONvergence of iterated CORrelations (CONCOR) R function

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KNOKE BUREAUCRACIES network data used here were obtained through UCINET software.

For an excellent method tutorial on blockmodeling with UCINET see the file Blockmodels.doc written by David Knoke and hosted on his SOC 8412 homepage.

# Stack matricies and matrix transposes
KNOKI <- read.table("KNOKI.txt",header=FALSE,sep="")
KNOKM <- read.table("KNOKM.txt",header=FALSE,sep="")
KNOKIT <- t(KNOKI)
KNOKMT <- t(KNOKM)
KNOK <- rbind(KNOKI,KNOKIT,KNOKM,KNOKMT)

# CONCOR function
# CONvergence of iterated CORrelations
# Creates a square matrix of correlations of the column pairs of a matrix
CONCOR <- function(mat){
    colN <- ncol(mat)
    X <- matrix(rep(0,times=colN*colN),nrow=colN,ncol=colN)
    for(i in 1:colN){
        for(j in i:colN){
            X[i,j] <- cor(mat[,i],mat[,j],method=c("pearson"))
        }
    }
    X <- X+(t(X)-diag(diag((X))))
return(X)
}

KNOKSIM <- CONCOR(KNOK)