Network graphs from adjacency matrix! (II)

networkII.R

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### Network graphs from adjacency matrix - II part ##
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# Author: Aurora-Mareviv
# Under GNU General Public License
# If we must construct an adjacency matrix:
# May be the cleanest way to plot links using igraph
# This Gist uses almost the same code as: https://gist.github.com/aurora-mareviv/5568957#file-gistfile1-r
# Paste and execute this simple code in a R console:

library(igraph)

# Let's construct an adjacency matrix:
pubId <- c(
1,2,3,4,5,6,7,8,9,10,12,13,14,15,16,17,18,19,20,21,22,23,24,
25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,
48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,
71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,
94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,
117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,
140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,
163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,
186,187,188,189,190,191,192,193,194,195,196,197,198,200,201,202,203,204,205,206,207,208,209,
210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,
233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,
256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,
279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303)

A001 <- c(
1,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,
0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,1,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,
1,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,
0,0,0,0,0,0,1,0,1,1)

A002 <- c(
0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,1,1,0,1,1,0,0,0,1,1,0,1,0,1,0,0,0,1,0,0,0,1,1,1,1,0,0,0,0,0,0,0,0,1,0,0,0,1,1,1,0,0,0,
0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,0,1,0,0,0,0,0,1,1,0,1,1,0,0,0,1,0,0,0,1,0,0,1,1,1,1,0,0,0,0,1,1,0,0,1,0,0,0,0,1,0,1,
0,1,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,1,0,1,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,1,1,1,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,1,1,1,
0,0,1,1,0,1,0,0,0,0,0,1,1,0,1,1,1,0,1,0,0,0,0,0,0,1,1,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,
1,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,1,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,1,1,0,0,0,1,1,1,0,1,0,
0,0,1,1,1,1,1,0,0,0)

A003 <- c(
0,1,1,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,1,1,1,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,
1,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,0,0,1,1,0,0,0,
0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,
1,1,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,1,1,1,1,1,0,0,0,0,0,1,0,1,1,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,1,
0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,1,1,0,1,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,
1,0,0,0,0,0,0,0,0,0)

A004 <- c(
0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,
0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,
0,0,1,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,1,0,0)

matx <- data.frame(pubId, A001, A002, A003, A004)
head(matx)
matx <- as.matrix(matx)
matx <- matx[,c(2,3,4,5)]


# An adjacency matrix looks like this!:
adj_mat = t(matx) %*% (matx)
adj_mat

# Adj_mat shows the number or connections between each node A001, A002...
# The connections are reciprocal, so the matrix is symmetrical.
# Now we will plot this matrix.
# Two ways to show edge weights:
 
# png("igraphs.png", width=10, height=5, units="in", res=200)
# par(mfrow=c(1, 2))
 
g1 = graph.adjacency(adj_mat, mode="undirected", diag=FALSE, weighted=TRUE)
plot(g1, edge.width=E(g1)$weight, vertex.size=50)
 
g2 = graph.adjacency(adj_mat, mode="undirected", diag=FALSE)
plot(g2, vertex.size=50)

# dev.off()


# "igraph" has another option: a GUI in tk:
tkplot(g2) # shows the window where you can manipulate the elements in the graph
coords1 <- tkplot.getcoords(1) # gets the coordinates to paste into another plot (see: https://gist.github.com/aurora-mareviv/5568957#file-gistfile1-r)