library("sand", lib.loc="~/R/win-library/3.1")
## Loading required package: igraph
##
## Attaching package: 'igraph'
##
## The following objects are masked from 'package:stats':
##
## decompose, spectrum
##
## The following object is masked from 'package:base':
##
## union
##
## Loading required package: igraphdata
##
## Statistical Analysis of Network Data with R
## Type in C2 (+ENTER) to start with Chapter 2.
library("rgl", lib.loc="~/R/win-library/3.1")
library("igraph", lib.loc="~/R/win-library/3.1")
g <- graph.formula(1-2, 1-3, 2-3, 2-4, 3-5, 4-5, 4-6,4-7, 5-6, 6-7)
g
## IGRAPH UN-- 7 10 --
## + attr: name (v/c)
## + edges (vertex names):
## [1] 1--2 1--3 2--3 2--4 3--5 4--5 4--6 4--7 5--6 6--7
V(g)
## + 7/7 vertices, named:
## [1] 1 2 3 4 5 6 7
E(g)
## + 10/10 edges (vertex names):
## [1] 1--2 1--3 2--3 2--4 3--5 4--5 4--6 4--7 5--6 6--7
str(g)
## IGRAPH UN-- 7 10 --
## + attr: name (v/c)
## + edges (vertex names):
## 1 -- 2, 3
## 2 -- 1, 3, 4
## 3 -- 1, 2, 5
## 4 -- 2, 5, 6, 7
## 5 -- 3, 4, 6
## 6 -- 4, 5, 7
## 7 -- 4, 6
g1 <- graph.formula(1-5, 1-7, 2-9, 2-4, 3-5, 4-5, 4-6,4-7, 5-6, 6-7,7-8,8-9)
g1
## IGRAPH UN-- 9 12 --
## + attr: name (v/c)
## + edges (vertex names):
## [1] 1--5 1--7 5--4 5--3 5--6 7--4 7--6 7--8 2--9 2--4 9--8 4--6
V(g1)
## + 9/9 vertices, named:
## [1] 1 5 7 2 9 4 3 6 8
E(g1)
## + 12/12 edges (vertex names):
## [1] 1--5 1--7 5--4 5--3 5--6 7--4 7--6 7--8 2--9 2--4 9--8 4--6
str(g1)
## IGRAPH UN-- 9 12 --
## + attr: name (v/c)
## + edges (vertex names):
## [1] 1--5 1--7 5--4 5--3 5--6 7--4 7--6 7--8 2--9 2--4 9--8 4--6
plot(g1)
rglplot(g1)
g2 <- make_lattice( c(5,5,5) )
coords <- layout_with_fr(g2, dim=3)
rglplot(g2, layout=coords)
str(g2)
## IGRAPH U--- 125 300 -- Lattice graph
## + attr: name (g/c), dimvector (g/n), nei (g/n), mutual (g/l),
## | circular (g/l)
## + edges:
## 1 -- 2 6 26 2 -- 1 3 7 27
## 3 -- 2 4 8 28 4 -- 3 5 9 29
## 5 -- 4 10 30 6 -- 1 7 11 31
## 7 -- 2 6 8 12 32 8 -- 3 7 9 13 33
## 9 -- 4 8 10 14 34 10 -- 5 9 15 35
## 11 -- 6 12 16 36 12 -- 7 11 13 17 37
## 13 -- 8 12 14 18 38 14 -- 9 13 15 19 39
## 15 -- 10 14 20 40 16 -- 11 17 21 41
## 17 -- 12 16 18 22 42 18 -- 13 17 19 23 43
## 19 -- 14 18 20 24 44 20 -- 15 19 25 45
## 21 -- 16 22 46 22 -- 17 21 23 47
## 23 -- 18 22 24 48 24 -- 19 23 25 49
## 25 -- 20 24 50 26 -- 1 27 31 51
## 27 -- 2 26 28 32 52 28 -- 3 27 29 33 53
## 29 -- 4 28 30 34 54 30 -- 5 29 35 55
## 31 -- 6 26 32 36 56 32 -- 7 27 31 33 37 57
## 33 -- 8 28 32 34 38 58 34 -- 9 29 33 35 39 59
## 35 -- 10 30 34 40 60 36 -- 11 31 37 41 61
## 37 -- 12 32 36 38 42 62 38 -- 13 33 37 39 43 63
## 39 -- 14 34 38 40 44 64 40 -- 15 35 39 45 65
## 41 -- 16 36 42 46 66 42 -- 17 37 41 43 47 67
## 43 -- 18 38 42 44 48 68 44 -- 19 39 43 45 49 69
## 45 -- 20 40 44 50 70 46 -- 21 41 47 71
## 47 -- 22 42 46 48 72 48 -- 23 43 47 49 73
## 49 -- 24 44 48 50 74 50 -- 25 45 49 75
## 51 -- 26 52 56 76 52 -- 27 51 53 57 77
## 53 -- 28 52 54 58 78 54 -- 29 53 55 59 79
## 55 -- 30 54 60 80 56 -- 31 51 57 61 81
## 57 -- 32 52 56 58 62 82 58 -- 33 53 57 59 63 83
## 59 -- 34 54 58 60 64 84 60 -- 35 55 59 65 85
## 61 -- 36 56 62 66 86 62 -- 37 57 61 63 67 87
## 63 -- 38 58 62 64 68 88 64 -- 39 59 63 65 69 89
## 65 -- 40 60 64 70 90 66 -- 41 61 67 71 91
## 67 -- 42 62 66 68 72 92 68 -- 43 63 67 69 73 93
## 69 -- 44 64 68 70 74 94 70 -- 45 65 69 75 95
## 71 -- 46 66 72 96 72 -- 47 67 71 73 97
## 73 -- 48 68 72 74 98 74 -- 49 69 73 75 99
## 75 -- 50 70 74 100 76 -- 51 77 81 101
## 77 -- 52 76 78 82 102 78 -- 53 77 79 83 103
## 79 -- 54 78 80 84 104 80 -- 55 79 85 105
## 81 -- 56 76 82 86 106 82 -- 57 77 81 83 87 107
## 83 -- 58 78 82 84 88 108 84 -- 59 79 83 85 89 109
## 85 -- 60 80 84 90 110 86 -- 61 81 87 91 111
## 87 -- 62 82 86 88 92 112 88 -- 63 83 87 89 93 113
## 89 -- 64 84 88 90 94 114 90 -- 65 85 89 95 115
## 91 -- 66 86 92 96 116 92 -- 67 87 91 93 97 117
## 93 -- 68 88 92 94 98 118 94 -- 69 89 93 95 99 119
## 95 -- 70 90 94 100 120 96 -- 71 91 97 121
## 97 -- 72 92 96 98 122 98 -- 73 93 97 99 123
## 99 -- 74 94 98 100 124 100 -- 75 95 99 125
## 101 -- 76 102 106 102 -- 77 101 103 107
## 103 -- 78 102 104 108 104 -- 79 103 105 109
## 105 -- 80 104 110 106 -- 81 101 107 111
## 107 -- 82 102 106 108 112 108 -- 83 103 107 109 113
## 109 -- 84 104 108 110 114 110 -- 85 105 109 115
## 111 -- 86 106 112 116 112 -- 87 107 111 113 117
## 113 -- 88 108 112 114 118 114 -- 89 109 113 115 119
## 115 -- 90 110 114 120 116 -- 91 111 117 121
## 117 -- 92 112 116 118 122 118 -- 93 113 117 119 123
## 119 -- 94 114 118 120 124 120 -- 95 115 119 125
## 121 -- 96 116 122 122 -- 97 117 121 123
## 123 -- 98 118 122 124 124 -- 99 119 123 125
## 125 -- 100 120 124
V(g2)$name <- c("Sam", "Mary", "Tom","3","4","5")
## Warning in vattrs[[name]][index] <- value: number of items to replace is
## not a multiple of replacement length
magact96 = read.delim("http://sna.stanford.edu/sna_R_labs/data/mag_act96.txt", na.strings = "na", check.names = FALSE)
magact97 = read.delim("http://sna.stanford.edu/sna_R_labs/data/mag_act97.txt", na.strings = "na", check.names = FALSE)
magact98 = read.delim("http://sna.stanford.edu/sna_R_labs/data/mag_act98.txt", na.strings = "na", check.names = FALSE)
magattrib = magact96[,1:4]
g96 <- as.matrix(magact96[,-(1:4)]); row.names(g96) = magact96[,1]
g97 <- as.matrix(magact97[,-(1:4)]); row.names(g97) = magact97[,1]
g98 <- as.matrix(magact98[,-(1:4)]); row.names(g98) = magact98[,1]
ig96 <- graph.incidence(g96, mode=c("all") )
ig97 <- graph.incidence(g97, mode=c("all") )
ig98 <- graph.incidence(g98, mode=c("all") )
V(ig96)$color[1:1294] = rgb(red = 1, green = 0, blue = 0, alpha = .5)
## Warning in vattrs[[name]][index] <- value: number of items to replace is
## not a multiple of replacement length
V(ig96)$color[1]
## [1] "#FF000080"
V(ig96)$color[2]
## [1] "#FF000080"
V(ig96)$color[120]
## [1] "#FF000080"
V(ig96)$color[1295:1385] = rgb(red = 0, green = 1, blue = 0, alpha = .5)
V(ig96)$color[1296]
## [1] "#00FF0080"
V(ig96)$color[1297]
## [1] "#00FF0080"
V(ig96)$label = V(ig96)$name
V(ig96)$label.color = rgb(0,0,.2,.5)
V(ig96)$label.cex = .4
V(ig96)$size = 6
V(ig96)$frame.color = V(ig96)$color
E(ig96)$color = rgb(.5,.5,0,.2)
pdf("lab5-ig96.pdf")
plot(ig96, layout=layout.fruchterman.reingold)
dev.off()
## png
## 2
pdf("lab5-ig96_kamada.pdf")
plot(ig96, layout=layout.kamada.kawai)
dev.off()
## png
## 2
jpeg("lab5-ig96_kamada.jpg")
plot(ig96, layout=layout.kamada.kawai)
dev.off()
## png
## 2