igraph.R
In igraph: Network Analysis and Visualization

## ----echo = TRUE, eval = FALSE------------------------------------------------
#  install.packages("igraph")

## ----echo = FALSE-------------------------------------------------------------
knitr::opts_chunk$set(fig.width=6, fig.height=6)

## ----setup--------------------------------------------------------------------
library("igraph")

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g <- make_empty_graph()

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g <- make_graph(edges = c(1,2, 1,5), n=10, directed = FALSE)

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g <- make_graph(~ 1--2, 1--5, 3, 4, 5, 6, 7, 8, 9, 10)

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g

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summary(g)

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g <- make_graph('Zachary')

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plot(g)

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g <- add_vertices(g, 3)

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g <- add_edges(g, edges = c(1,35, 1,36, 34,37))

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#  g <- g + edges(c(1,35, 1,36, 34,37))

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#  g <- add_edges(g, edges = c(38,37))

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g <- g %>% add_edges(edges=c(1,34)) %>% add_vertices(3) %>%
     add_edges(edges=c(38,39, 39,40, 40,38, 40,37))
g

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get.edge.ids(g, c(1,34))

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g <- delete_edges(g, 82)

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g <- make_ring(10) %>% delete_edges("10|1")
plot(g)

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g <- make_ring(5)
g <- delete_edges(g, get.edge.ids(g, c(1,5, 4,5)))
plot(g)

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g1 <- graph_from_literal(A-B:C:I, B-A:C:D, C-A:B:E:H, D-B:E:F,
                         E-C:D:F:H, F-D:E:G, G-F:H, H-C:E:G:I,
                         I-A:H)
plot(g1)

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is_chordal(g1, fillin=TRUE)

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chordal_graph <- add_edges(g1, is_chordal(g1, fillin=TRUE)$fillin)
plot(chordal_graph)

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graph1 <- make_tree(127, 2, mode = "undirected")
summary(g)

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graph2 <- make_tree(127, 2, mode = "undirected")

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identical_graphs(graph1,graph2)

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graph1 <- sample_grg(100, 0.2)
summary(graph1)

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graph2 <- sample_grg(100, 0.2)
identical_graphs(graph1, graph2)

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isomorphic(graph1, graph2)

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g <- make_graph(~ Alice-Bob:Claire:Frank, Claire-Alice:Dennis:Frank:Esther,
                George-Dennis:Frank, Dennis-Esther)

## ----echo = TRUE--------------------------------------------------------------
V(g)$age <- c(25, 31, 18, 23, 47, 22, 50) 
V(g)$gender <- c("f", "m", "f", "m", "m", "f", "m")
E(g)$is_formal <- c(FALSE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE)
summary(g)

## ----echo = TRUE, eval=FALSE--------------------------------------------------
#  g <- make_graph(~ Alice-Bob:Claire:Frank, Claire-Alice:Dennis:Frank:Esther,
#                  George-Dennis:Frank, Dennis-Esther) %>%
#    set_vertex_attr("age", value = c(25, 31, 18, 23, 47, 22, 50)) %>%
#    set_vertex_attr("gender", value = c("f", "m", "f", "m", "m", "f", "m")) %>%
#    set_edge_attr("is_formal", value = c(FALSE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE))
#  summary(g)

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E(g)$is_formal
E(g)$is_formal[1] <- TRUE
E(g)$is_formal

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g$date <- c("2022-02-11")
graph_attr(g, "date")

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match(c("George"), V(g)$name)

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V(g)$name[1:3] <- c("Alejandra", "Bruno", "Carmina")
V(g)

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g <- delete_vertex_attr(g, "gender")
V(g)$gender

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degree(g)

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degree(g, 7)

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degree(g, v=c(3,4,5))

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degree(g, v=c("Carmina", "Frank", "Dennis"))

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degree(g, "Bruno")

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edge_betweenness(g)

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ebs <- edge_betweenness(g)
as_edgelist(g)[ebs == max(ebs), ]

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which.max(degree(g))

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graph <- graph.full(n=10)
only_odd_vertices <- which(V(graph)%%2==1)
length(only_odd_vertices)

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seq <- V(graph)[2, 3, 7]
seq

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seq <- seq[1, 3]    # filtering an existing vertex set
seq

## ----echo = TRUE, eval = FALSE------------------------------------------------
#  seq <- V(graph)[2, 3, 7, "foo", 3.5]
#  ## Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected

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V(g)[age < 30]$name

## ----echo = TRUE--------------------------------------------------------------
`%notin%` <- Negate(`%in%`)

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V(g)$degree <- c("A", "B", "B+", "A+", "C", "A", "B")
V(g)$degree[degree(g) == 3]

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V(g)$name[degree(g) == 3]

## ----echo = TRUE, warning = FALSE---------------------------------------------
E(g)[.from(3)]

## ----echo = TRUE, warning = FALSE---------------------------------------------
E(g)[.from("Carmina")]

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E(g) [ 3:5 %--% 5:6 ]

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V(g)$gender <- c("f", "m", "f", "m", "m", "f", "m")

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men <- V(g)[gender == "m"]$name
men

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women <- V(g)[gender == "f"]$name
women

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E(g)[men %--% women]

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get.adjacency(g)

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layout <- layout_with_kk(g)

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layout <- layout_as_tree(g, root = 2)

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layout <- layout_with_kk(g)

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plot(g, layout = layout, main = "Social network with the Kamada-Kawai layout algorithm")

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plot(g, layout = layout_with_fr,
     main = "Social network with the Fruchterman-Reingold layout algorithm")

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V(g)$color <- ifelse(V(g)$gender == "m", "yellow", "red")
plot(g, layout = layout, vertex.label.dist = 3.5,
     main = "Social network - with genders as colors")

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plot(g, layout=layout, vertex.label.dist=3.5, vertex.color=as.factor(V(g)$gender))

## -----------------------------------------------------------------------------
plot(g, layout=layout, vertex.label.dist=3.5, vertex.size=20,
     vertex.color=ifelse(V(g)$gender == "m", "yellow", "red"),
     edge.width=ifelse(E(g)$is_formal, 5, 1))

## ----session-info-------------------------------------------------------------
sessionInfo()