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))

## ----echo = TRUE, eval=FALSE--------------------------------------------------
#  g <- g + edges(c(1, 35, 1, 36, 34, 37))

## ----echo = TRUE, error = TRUE------------------------------------------------
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

## ----echo = TRUE--------------------------------------------------------------
edge_id_to_delete <- get_edge_ids(g, c(1, 34))
edge_id_to_delete

## -----------------------------------------------------------------------------
g <- delete_edges(g, edge_id_to_delete)

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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)

## -----------------------------------------------------------------------------
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(graph1)

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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)

## ----echo = TRUE--------------------------------------------------------------
isomorphic(graph1, graph2)

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g <- make_graph(
  ~ Alice - Boris:Himari:Moshe, Himari - Alice:Nang:Moshe:Samira,
  Ibrahim - Nang:Moshe, Nang - Samira
)

## ----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 - Boris:Himari:Moshe, Himari - Alice:Nang:Moshe:Samira,
#    Ibrahim - Nang:Moshe, Nang - Samira
#  ) %>%
#    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)

## ----echo = TRUE--------------------------------------------------------------
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("Ibrahim"), 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", "Moshe", "Nang"))

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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)

## ----echo = TRUE--------------------------------------------------------------
seq <- V(graph)[2, 3, 7]
seq

## ----echo = TRUE--------------------------------------------------------------
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

## ----echo = TRUE--------------------------------------------------------------
V(g)[age < 30]$name

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

## ----echo = TRUE--------------------------------------------------------------
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")]

## ----echo = TRUE--------------------------------------------------------------
E(g)[3:5 %--% 5:6]

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

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

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

## ----echo = TRUE--------------------------------------------------------------
E(g)[men %--% women]

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as_adjacency_matrix(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")

## -----------------------------------------------------------------------------
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"
)

## -----------------------------------------------------------------------------
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()