Добавьте метки в дендрограмму и раскрасьте кластеры

Question

Добавьте метки в дендрограмму и раскрасьте кластеры

Я создаю дендрограмму, используя ggdendro в этом случае:

library(igraph)
library(RColorBrewer)
library(GGally)
library(ggplot2)
library(plotrix)
library(extrafont)
library(ggdendro)

# load dataset
net <- read.graph("./dataset/lesmiserables.gml", format = c("gml"))
deg <- igraph::degree(net, mode = "all")

# find communities
girvNew <- cluster_edge_betweenness(net)

girvNew_sizesComm <- sizes(girvNew)
girvNew_numComm <- length(girvNew_sizesComm)

# colors
colorsRainbow <- rainbow(max(membership(girvNew)), alpha = 0.6)

x11()
plot(net,
     vertex.size = plotrix::rescale(deg, c(5, 16)),
     vertex.color = colorsRainbow[membership(girvNew)],
     vertex.frame.color = NA,
     vertex.label = NA,
     vertex.size = 10,
     edge.color = "#d8d8d8",
     layout = layout.fruchterman.reingold,
     main = "Detected communities")

# find dendrogram
girvNew_den <- as.dendrogram(girvNew)

#convert cluster object to use with ggplot
girvNew_dendrogram <- dendro_data(girvNew_den, type = "rectangle") 

x11()
ggdendrogram(girvNew_dendrogram, 
             rotate = TRUE, 
             labels = TRUE,
             segments = TRUE,
             leaf_labels = TRUE, 
             theme_dendro = FALSE)

И я получаю:

Моя сеть:

> dput(net)
structure(list(77, FALSE, c(1, 2, 3, 3, 4, 5, 6, 7, 8, 9, 11, 
11, 11, 11, 12, 13, 14, 15, 17, 18, 18, 19, 19, 19, 20, 20, 20, 
20, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 
23, 23, 23, 23, 23, 24, 24, 25, 25, 25, 26, 26, 26, 26, 27, 27, 
27, 27, 27, 28, 28, 29, 29, 29, 30, 31, 31, 31, 31, 32, 33, 33, 
34, 34, 35, 35, 35, 36, 36, 36, 36, 37, 37, 37, 37, 37, 38, 38, 
38, 38, 38, 38, 39, 40, 41, 41, 42, 42, 42, 43, 43, 43, 44, 44, 
45, 47, 48, 48, 48, 48, 49, 49, 50, 50, 51, 51, 51, 52, 52, 53, 
54, 54, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 56, 56, 57, 
57, 57, 58, 58, 58, 58, 58, 59, 59, 59, 59, 60, 60, 60, 61, 61, 
61, 61, 61, 61, 62, 62, 62, 62, 62, 62, 62, 62, 63, 63, 63, 63, 
63, 63, 63, 63, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 65, 65, 
65, 65, 65, 65, 65, 65, 65, 65, 66, 66, 66, 66, 66, 66, 66, 66, 
66, 67, 68, 68, 68, 68, 68, 68, 69, 69, 69, 69, 69, 69, 69, 70, 
70, 70, 70, 70, 70, 70, 70, 71, 71, 71, 71, 71, 71, 71, 71, 72, 
72, 72, 73, 74, 74, 75, 75, 75, 75, 75, 75, 75, 76, 76, 76, 76, 
76, 76, 76), c(0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 10, 3, 2, 0, 11, 
11, 11, 11, 16, 16, 17, 16, 17, 18, 16, 17, 18, 19, 16, 17, 18, 
19, 20, 16, 17, 18, 19, 20, 21, 16, 17, 18, 19, 20, 21, 22, 12, 
11, 23, 11, 24, 23, 11, 24, 11, 16, 25, 11, 23, 25, 24, 26, 11, 
27, 23, 27, 11, 23, 30, 11, 23, 27, 11, 11, 27, 11, 29, 11, 34, 
29, 34, 35, 11, 29, 34, 35, 36, 11, 29, 34, 35, 36, 37, 11, 29, 
25, 25, 24, 25, 41, 25, 24, 11, 26, 27, 28, 11, 28, 46, 47, 25, 
27, 11, 26, 11, 49, 24, 49, 26, 11, 51, 39, 51, 51, 49, 26, 51, 
49, 39, 54, 26, 11, 16, 25, 41, 48, 49, 55, 55, 41, 48, 55, 48, 
27, 57, 11, 58, 55, 48, 57, 48, 58, 59, 48, 58, 60, 59, 57, 55, 
55, 58, 59, 48, 57, 41, 61, 60, 59, 48, 62, 57, 58, 61, 60, 55, 
55, 62, 48, 63, 58, 61, 60, 59, 57, 11, 63, 64, 48, 62, 58, 61, 
60, 59, 57, 55, 64, 58, 59, 62, 65, 48, 63, 61, 60, 57, 25, 11, 
24, 27, 48, 41, 25, 68, 11, 24, 27, 48, 41, 25, 69, 68, 11, 24, 
27, 41, 58, 27, 69, 68, 70, 11, 48, 41, 25, 26, 27, 11, 48, 48, 
73, 69, 68, 25, 48, 41, 70, 71, 64, 65, 66, 63, 62, 48, 58), 
    c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 12, 11, 10, 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, 47, 46, 39, 40, 41, 42, 43, 44, 
    45, 49, 48, 52, 51, 50, 54, 55, 53, 56, 57, 58, 60, 59, 61, 
    62, 63, 66, 64, 65, 67, 69, 70, 71, 68, 72, 73, 74, 75, 76, 
    77, 79, 78, 82, 83, 80, 81, 87, 88, 84, 85, 86, 93, 94, 89, 
    90, 91, 92, 95, 96, 97, 98, 101, 100, 99, 102, 103, 104, 
    106, 105, 107, 108, 112, 110, 111, 109, 114, 113, 116, 115, 
    119, 118, 117, 121, 120, 122, 125, 124, 123, 131, 132, 133, 
    130, 128, 134, 135, 127, 126, 129, 136, 137, 139, 140, 138, 
    145, 143, 142, 141, 144, 148, 147, 149, 146, 150, 151, 152, 
    153, 158, 157, 154, 156, 155, 164, 162, 159, 163, 160, 161, 
    166, 165, 168, 174, 170, 171, 167, 173, 172, 169, 184, 177, 
    175, 183, 179, 182, 181, 180, 176, 178, 187, 194, 193, 189, 
    192, 191, 190, 188, 185, 186, 200, 196, 197, 203, 202, 198, 
    201, 195, 199, 204, 206, 207, 205, 208, 210, 209, 213, 214, 
    211, 215, 217, 216, 212, 221, 222, 218, 223, 224, 225, 220, 
    219, 230, 233, 226, 232, 231, 228, 227, 229, 236, 234, 235, 
    237, 238, 239, 242, 244, 243, 241, 240, 245, 246, 252, 253, 
    251, 250, 247, 248, 249), c(0, 1, 2, 4, 5, 6, 7, 8, 9, 13, 
    3, 12, 11, 10, 14, 15, 16, 17, 47, 49, 52, 54, 57, 62, 66, 
    69, 72, 73, 75, 77, 82, 87, 93, 102, 106, 112, 114, 119, 
    131, 145, 184, 206, 213, 221, 230, 236, 46, 18, 19, 21, 24, 
    28, 33, 39, 55, 132, 20, 22, 25, 29, 34, 40, 23, 26, 30, 
    35, 41, 27, 31, 36, 42, 32, 37, 43, 38, 44, 45, 48, 51, 58, 
    64, 67, 70, 50, 53, 60, 97, 101, 116, 207, 214, 222, 56, 
    59, 95, 96, 98, 100, 110, 133, 205, 211, 218, 233, 242, 61, 
    103, 113, 118, 125, 130, 234, 63, 65, 71, 74, 104, 111, 143, 
    208, 215, 223, 226, 235, 105, 107, 76, 79, 83, 88, 94, 68, 
    78, 80, 84, 89, 81, 85, 90, 86, 91, 92, 121, 128, 99, 134, 
    139, 164, 210, 217, 224, 232, 244, 108, 109, 135, 140, 142, 
    148, 150, 153, 162, 168, 177, 187, 200, 209, 216, 231, 237, 
    238, 243, 252, 115, 117, 124, 127, 136, 120, 122, 123, 126, 
    129, 137, 138, 141, 147, 158, 159, 174, 175, 194, 144, 149, 
    157, 163, 170, 183, 193, 204, 146, 151, 154, 160, 171, 179, 
    189, 196, 225, 253, 152, 156, 161, 167, 182, 192, 197, 155, 
    166, 173, 181, 191, 203, 165, 172, 180, 190, 202, 169, 176, 
    188, 198, 251, 178, 185, 201, 250, 186, 195, 247, 199, 248, 
    249, 212, 220, 228, 241, 219, 227, 240, 229, 245, 246, 239
    ), c(0, 0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 10, 14, 15, 16, 17, 
    18, 18, 19, 21, 24, 28, 33, 39, 48, 50, 53, 57, 62, 64, 67, 
    68, 72, 73, 75, 77, 80, 84, 89, 95, 96, 97, 99, 102, 105, 
    107, 108, 108, 109, 113, 115, 117, 120, 122, 123, 126, 136, 
    138, 141, 146, 150, 153, 159, 167, 175, 185, 195, 204, 205, 
    211, 218, 226, 234, 237, 238, 240, 247, 254), c(0, 10, 10, 
    12, 13, 13, 13, 13, 13, 13, 13, 14, 46, 47, 47, 47, 47, 56, 
    62, 67, 71, 74, 76, 77, 83, 92, 105, 112, 124, 126, 131, 
    132, 132, 132, 132, 136, 139, 141, 142, 142, 144, 144, 153, 
    153, 153, 153, 153, 154, 155, 173, 178, 178, 182, 182, 182, 
    183, 192, 192, 200, 210, 217, 223, 228, 233, 237, 240, 242, 
    243, 243, 247, 250, 252, 253, 253, 254, 254, 254, 254), list(
        c(1, 0, 1), structure(list(), .Names = character(0)), 
        structure(list(id = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 
        11, 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), label = c("Myriel", 
        "Napoleon", "MlleBaptistine", "MmeMagloire", "CountessDeLo", 
        "Geborand", "Champtercier", "Cravatte", "Count", "OldMan", 
        "Labarre", "Valjean", "Marguerite", "MmeDeR", "Isabeau", 
        "Gervais", "Tholomyes", "Listolier", "Fameuil", "Blacheville", 
        "Favourite", "Dahlia", "Zephine", "Fantine", "MmeThenardier", 
        "Thenardier", "Cosette", "Javert", "Fauchelevent", "Bamatabois", 
        "Perpetue", "Simplice", "Scaufflaire", "Woman1", "Judge", 
        "Champmathieu", "Brevet", "Chenildieu", "Cochepaille", 
        "Pontmercy", "Boulatruelle", "Eponine", "Anzelma", "Woman2", 
        "MotherInnocent", "Gribier", "Jondrette", "MmeBurgon", 
        "Gavroche", "Gillenormand", "Magnon", "MlleGillenormand", 
        "MmePontmercy", "MlleVaubois", "LtGillenormand", "Marius", 
        "BaronessT", "Mabeuf", "Enjolras", "Combeferre", "Prouvaire", 
        "Feuilly", "Courfeyrac", "Bahorel", "Bossuet", "Joly", 
        "Grantaire", "MotherPlutarch", "Gueulemer", "Babet", 
        "Claquesous", "Montparnasse", "Toussaint", "Child1", 
        "Child2", "Brujon", "MmeHucheloup"), maincharacter = c(0, 
        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 
        0, 0, 0, 0, 1, 0, 1, 1, 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, 
        1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
        0, 0, 0, 0)), .Names = c("id", "label", "maincharacter"
        )), structure(list(value = c(1, 8, 10, 6, 1, 1, 1, 1, 
        2, 1, 1, 3, 3, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 3, 3, 
        3, 4, 3, 3, 3, 3, 5, 3, 3, 3, 3, 4, 4, 3, 3, 3, 3, 4, 
        4, 4, 2, 9, 2, 7, 13, 1, 12, 4, 31, 1, 1, 17, 5, 5, 1, 
        1, 8, 1, 1, 1, 2, 1, 2, 3, 2, 1, 1, 2, 1, 3, 2, 3, 3, 
        2, 2, 2, 2, 1, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 1, 1, 1, 
        2, 3, 2, 2, 1, 3, 1, 1, 3, 1, 2, 1, 2, 1, 1, 1, 3, 2, 
        1, 1, 9, 2, 2, 1, 1, 1, 2, 1, 1, 6, 12, 1, 1, 21, 19, 
        1, 2, 5, 4, 1, 1, 1, 1, 1, 7, 7, 6, 1, 4, 15, 5, 6, 2, 
        1, 4, 2, 2, 6, 2, 5, 1, 1, 9, 17, 13, 7, 2, 1, 6, 3, 
        5, 5, 6, 2, 4, 3, 2, 1, 5, 12, 5, 4, 10, 6, 2, 9, 1, 
        1, 5, 7, 3, 5, 5, 5, 2, 5, 1, 2, 3, 3, 1, 2, 2, 1, 1, 
        1, 1, 3, 5, 1, 1, 1, 1, 1, 6, 6, 1, 1, 2, 1, 1, 4, 4, 
        4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 1, 1, 2, 
        2, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .Names = "value")), 
    <environment>), class = "igraph")

Хотелось бы, чтобы на вертикальной оси были имена узлов сети, а линии кластеров одного цвета для сообществ, рассчитанных с cluster_edge_betweenness функция.

Это действительно не имеет значения, если они красочные:

узлы (метки) или
линии кластеров или
фон каждого кластера.

Важно то, что я могу различать кластеры на основе цветов, как я могу сделать на первом графике (с круглыми узлами).

Как я могу сделать? Я искал в Интернете, но я не мог решить. Спасибо

Я пытался следовать обеим этим дорогам:

после ответа jlhoward в этом посте
использовать пакет dendextend

У меня были проблемы с самого начала для обоих.

(1) В ответе df это фрейм данных, а у меня есть список (net), и я не знаю, как правильно преобразовать мою сеть во фрейм данных, как в примере. В любом случае, если я попытаюсь (просто играть) сделать rownames(df) <- V(net)$label я получил

Ошибка в row.names<-.data.frame (*tmp*, значение = значение): длина 'row.names' недопустима

Совершенно верно. Но намеченный результат таков:

Он не использует ярлык net сетевые узлы, но те из df сеть. Это кажется мне очень странным.

(2) Вот что я сделал:

library(igraph)
library(GGally)
library(ggplot2)
library(ggdendro)
library(dendextend)
library(dendextendRcpp)
library(zoo)

# load dataset
net <- read.graph("./dataset/lesmiserables.gml", format = c("gml"))
deg <- igraph::degree(net, mode = "all")

comm <- fastgreedy.community(net)

comm_sizesComm <- sizes(comm) 
comm_numComm <- length(comm_sizesComm)
comm_modularity <- modularity(comm)

# plot communities
colorsRainbow <- rainbow(max(membership(comm)), alpha = 0.6)
pdf(file = "./output/prova_comm2.pdf")
plot(net,
     vertex.size = plotrix::rescale(deg, c(5, 16)),
     vertex.color = colorsRainbow[membership(comm)],
     vertex.frame.color = NA,
     vertex.label.color = "black",
     vertex.label.cex = 0.5,
     vertex.size = 10,
     edge.color = "#d8d8d8",
     layout = layout.fruchterman.reingold,
     edge.curved = FALSE)
dev.off()

# create dendrogram
dend <- as.dendrogram(comm)

cut <- comm_numComm

# change labels
dend <- dend %>% set("labels", V(net)$label) # change label
dend <- dend %>% set("labels_col", "black") # change color 
dend <- dend %>% set("labels_cex", .5) # change size

# color label based on communities
colorsRainbow <- rainbow(max(membership(comm)), alpha = 1)
dend <- dend %>% set("labels_col", value = colorsRainbow, k = cut) 

# plot dendrogram
pdf(file = "./output/prova_dend2.pdf")
plot(dend, 
     horiz = TRUE,
     main = "Dendrogram")
dev.off()

Мне удалось изменить ярлык и покрасить их. Но цвета не совпадают между двумя графиками. Я не понимаю, проблема ли это в сюжете или построении дендограммы.

Объясните: на первом графике (с узлами, представленными точками) у меня есть то, что в синем сообществе есть узлы {Perpetual, Fantine, Anzelma, Simplice,...}. В жёлтой общине есть { Woman2, Marius, Magnon, Cosette,...}.

Если я сейчас увижу второй график (дендрограмму), я увижу, что узлы Woman2 и Anzelma находятся в двух разных сообществах. Это кажется огромной проблемой, и я не знаю, как начать решать.

(3) Я пробовал также:

ggd1 <- as.ggdend(dend)
ggplot(ggd1)

И проблема та же самая (2): сообщества не совпадают.

Я создаю этот простой график:

> dput(net)
structure(list(16, FALSE, c(1, 2, 3, 2, 3, 3, 4, 5, 5, 7, 7, 
9, 8, 10, 9, 11, 11, 14, 15, 15, 15, 12, 14), c(0, 0, 0, 1, 2, 
1, 3, 3, 4, 3, 6, 6, 7, 8, 8, 8, 10, 11, 14, 13, 12, 3, 1), c(0, 
1, 3, 2, 5, 4, 6, 7, 8, 9, 10, 12, 11, 14, 13, 15, 16, 21, 22, 
17, 20, 19, 18), c(0, 1, 2, 3, 5, 22, 4, 6, 7, 9, 21, 8, 10, 
11, 12, 14, 13, 15, 16, 17, 20, 19, 18), c(0, 0, 1, 3, 6, 7, 
9, 9, 11, 12, 14, 15, 17, 18, 18, 20, 23), c(0, 3, 6, 7, 11, 
12, 12, 14, 15, 18, 18, 19, 20, 21, 22, 23, 23), list(c(1, 0, 
1), structure(list(), .Names = character(0)), structure(list(
    id = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 
    15), label = c("A", "B", "C", "D", "E", "F", "G", "H", "I", 
    "L", "M", "N", "O", "P", "Q", "R")), .Names = c("id", "label"
)), list()), <environment>), class = "igraph")

а потом я нахожу сообщества и дендрограммы:

# calculate degree
deg <- igraph::degree(net, mode = "all")

# find communities
com <- cluster_edge_betweenness(net) 
## or use 
# com <- fastgreedy.community(net)

# details on communities
com_sizesCom <- sizes(com) 
com_numCom <- length(com_sizesCom)

# create dendrogram
dend <- as.dendrogram(com)
labels(dend) <- V(net)$label[order.dendrogram(dend)]

k <- max(membership(com))
colorsRainbow <- rainbow(k, alpha = 1)

set.seed(23420)
colorsRainbow <- rainbow(max(membership(com)))
colorsRainbow <- sample(colorsRainbow)
dend <- dend %>% set("labels_col", value = colorsRainbow, k = k)
dend <- dend %>% set("branches_k_color", value = colorsRainbow, k = k)
dend <- dend %>% set("labels_cex", 1)

Я получил:

Итак, цвета не верны.

Весь обновленный код. Теперь синий и зеленый поменялись местами.

 library(igraph)
 library(dendextend)
 library(colorspace)

 net <- upgrade_graph(net)
 # dput(net)

 # calculate degree
 deg <- igraph::degree(net, mode = "all")

 # plot network
 x11()
 plot(net,
      vertex.size = plotrix::rescale(deg, c(8, 22)),
      vertex.color = "tomato",
      vertex.frame.color = NA,
      vertex.label.color = "black",
      vertex.size = 10,
      edge.color = "#d8d8d8",
      layout = layout.fruchterman.reingold,
      edge.curved = FALSE)

 # find communities
 com <- cluster_edge_betweenness(net) 

 # details on communities
 com_sizesCom <- sizes(com) 
 com_numCom <- length(com_sizesCom)
 print(com_numCom)

 # plot communities
 colorsRainbow <- rainbow(max(membership(com)), alpha = 0.6)
 x11()
 par(mar = c(1, 1, 1, 1))
 plot(net,
      vertex.size = plotrix::rescale(deg, c(8, 22)),
      vertex.color = colorsRainbow[membership(com)],
      vertex.frame.color = NA,
      edge.color = "#d8d8d8",
      vertex.label.color = "black",
      layout = layout.fruchterman.reingold,
      edge.curved = FALSE)

 # create dendrogram
 dend <- as.dendrogram(com)
 labels(dend) <- V(net)$label[order.dendrogram(dend)]

 k <- max(membership(com))
 colorsRainbow <- rainbow(k, alpha = 1)

 colorsRainbow <- rev(unique(colorsRainbow[membership(com)[order.dendrogram(dend)]]))
 dend <- dend %>% set("labels_col", value = colorsRainbow, k = k)
 dend <- dend %>% set("branches_k_color", value = colorsRainbow, k = k)
 dend <- dend %>% set("labels_cex", 1)

 # plot dendrogram
 x11()
 par(mar = c(3, 1, 1, 5))
 plot(dend, horiz = T)

1

r ggplot2 igraph dendrogram ggdendro

Источник

user6131384 16 апр '16 в 18:30

1 ответ

Другие вопросы по тегам r ggplot2 igraph dendrogram ggdendro

user256662 17 апр '16 в 13:45 2016-04-17 13:45 · Answer 1 · 2016-04-17 13:45

Я не уверен, что правильно получил порядок меток (так как не уверен, как они извлекаются из сети), но вот попытка воспроизвести пример:

library(igraph)

net <- structure(list(77, FALSE, c(1, 2, 3, 3, 4, 5, 6, 7, 8, 9, 11, 
11, 11, 11, 12, 13, 14, 15, 17, 18, 18, 19, 19, 19, 20, 20, 20, 
20, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 
23, 23, 23, 23, 23, 24, 24, 25, 25, 25, 26, 26, 26, 26, 27, 27, 
27, 27, 27, 28, 28, 29, 29, 29, 30, 31, 31, 31, 31, 32, 33, 33, 
34, 34, 35, 35, 35, 36, 36, 36, 36, 37, 37, 37, 37, 37, 38, 38, 
38, 38, 38, 38, 39, 40, 41, 41, 42, 42, 42, 43, 43, 43, 44, 44, 
45, 47, 48, 48, 48, 48, 49, 49, 50, 50, 51, 51, 51, 52, 52, 53, 
54, 54, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 56, 56, 57, 
57, 57, 58, 58, 58, 58, 58, 59, 59, 59, 59, 60, 60, 60, 61, 61, 
61, 61, 61, 61, 62, 62, 62, 62, 62, 62, 62, 62, 63, 63, 63, 63, 
63, 63, 63, 63, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 65, 65, 
65, 65, 65, 65, 65, 65, 65, 65, 66, 66, 66, 66, 66, 66, 66, 66, 
66, 67, 68, 68, 68, 68, 68, 68, 69, 69, 69, 69, 69, 69, 69, 70, 
70, 70, 70, 70, 70, 70, 70, 71, 71, 71, 71, 71, 71, 71, 71, 72, 
72, 72, 73, 74, 74, 75, 75, 75, 75, 75, 75, 75, 76, 76, 76, 76, 
76, 76, 76), c(0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 10, 3, 2, 0, 11, 
11, 11, 11, 16, 16, 17, 16, 17, 18, 16, 17, 18, 19, 16, 17, 18, 
19, 20, 16, 17, 18, 19, 20, 21, 16, 17, 18, 19, 20, 21, 22, 12, 
11, 23, 11, 24, 23, 11, 24, 11, 16, 25, 11, 23, 25, 24, 26, 11, 
27, 23, 27, 11, 23, 30, 11, 23, 27, 11, 11, 27, 11, 29, 11, 34, 
29, 34, 35, 11, 29, 34, 35, 36, 11, 29, 34, 35, 36, 37, 11, 29, 
25, 25, 24, 25, 41, 25, 24, 11, 26, 27, 28, 11, 28, 46, 47, 25, 
27, 11, 26, 11, 49, 24, 49, 26, 11, 51, 39, 51, 51, 49, 26, 51, 
49, 39, 54, 26, 11, 16, 25, 41, 48, 49, 55, 55, 41, 48, 55, 48, 
27, 57, 11, 58, 55, 48, 57, 48, 58, 59, 48, 58, 60, 59, 57, 55, 
55, 58, 59, 48, 57, 41, 61, 60, 59, 48, 62, 57, 58, 61, 60, 55, 
55, 62, 48, 63, 58, 61, 60, 59, 57, 11, 63, 64, 48, 62, 58, 61, 
60, 59, 57, 55, 64, 58, 59, 62, 65, 48, 63, 61, 60, 57, 25, 11, 
24, 27, 48, 41, 25, 68, 11, 24, 27, 48, 41, 25, 69, 68, 11, 24, 
27, 41, 58, 27, 69, 68, 70, 11, 48, 41, 25, 26, 27, 11, 48, 48, 
73, 69, 68, 25, 48, 41, 70, 71, 64, 65, 66, 63, 62, 48, 58), 
    c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 12, 11, 10, 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, 47, 46, 39, 40, 41, 42, 43, 44, 
    45, 49, 48, 52, 51, 50, 54, 55, 53, 56, 57, 58, 60, 59, 61, 
    62, 63, 66, 64, 65, 67, 69, 70, 71, 68, 72, 73, 74, 75, 76, 
    77, 79, 78, 82, 83, 80, 81, 87, 88, 84, 85, 86, 93, 94, 89, 
    90, 91, 92, 95, 96, 97, 98, 101, 100, 99, 102, 103, 104, 
    106, 105, 107, 108, 112, 110, 111, 109, 114, 113, 116, 115, 
    119, 118, 117, 121, 120, 122, 125, 124, 123, 131, 132, 133, 
    130, 128, 134, 135, 127, 126, 129, 136, 137, 139, 140, 138, 
    145, 143, 142, 141, 144, 148, 147, 149, 146, 150, 151, 152, 
    153, 158, 157, 154, 156, 155, 164, 162, 159, 163, 160, 161, 
    166, 165, 168, 174, 170, 171, 167, 173, 172, 169, 184, 177, 
    175, 183, 179, 182, 181, 180, 176, 178, 187, 194, 193, 189, 
    192, 191, 190, 188, 185, 186, 200, 196, 197, 203, 202, 198, 
    201, 195, 199, 204, 206, 207, 205, 208, 210, 209, 213, 214, 
    211, 215, 217, 216, 212, 221, 222, 218, 223, 224, 225, 220, 
    219, 230, 233, 226, 232, 231, 228, 227, 229, 236, 234, 235, 
    237, 238, 239, 242, 244, 243, 241, 240, 245, 246, 252, 253, 
    251, 250, 247, 248, 249), c(0, 1, 2, 4, 5, 6, 7, 8, 9, 13, 
    3, 12, 11, 10, 14, 15, 16, 17, 47, 49, 52, 54, 57, 62, 66, 
    69, 72, 73, 75, 77, 82, 87, 93, 102, 106, 112, 114, 119, 
    131, 145, 184, 206, 213, 221, 230, 236, 46, 18, 19, 21, 24, 
    28, 33, 39, 55, 132, 20, 22, 25, 29, 34, 40, 23, 26, 30, 
    35, 41, 27, 31, 36, 42, 32, 37, 43, 38, 44, 45, 48, 51, 58, 
    64, 67, 70, 50, 53, 60, 97, 101, 116, 207, 214, 222, 56, 
    59, 95, 96, 98, 100, 110, 133, 205, 211, 218, 233, 242, 61, 
    103, 113, 118, 125, 130, 234, 63, 65, 71, 74, 104, 111, 143, 
    208, 215, 223, 226, 235, 105, 107, 76, 79, 83, 88, 94, 68, 
    78, 80, 84, 89, 81, 85, 90, 86, 91, 92, 121, 128, 99, 134, 
    139, 164, 210, 217, 224, 232, 244, 108, 109, 135, 140, 142, 
    148, 150, 153, 162, 168, 177, 187, 200, 209, 216, 231, 237, 
    238, 243, 252, 115, 117, 124, 127, 136, 120, 122, 123, 126, 
    129, 137, 138, 141, 147, 158, 159, 174, 175, 194, 144, 149, 
    157, 163, 170, 183, 193, 204, 146, 151, 154, 160, 171, 179, 
    189, 196, 225, 253, 152, 156, 161, 167, 182, 192, 197, 155, 
    166, 173, 181, 191, 203, 165, 172, 180, 190, 202, 169, 176, 
    188, 198, 251, 178, 185, 201, 250, 186, 195, 247, 199, 248, 
    249, 212, 220, 228, 241, 219, 227, 240, 229, 245, 246, 239
    ), c(0, 0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 10, 14, 15, 16, 17, 
    18, 18, 19, 21, 24, 28, 33, 39, 48, 50, 53, 57, 62, 64, 67, 
    68, 72, 73, 75, 77, 80, 84, 89, 95, 96, 97, 99, 102, 105, 
    107, 108, 108, 109, 113, 115, 117, 120, 122, 123, 126, 136, 
    138, 141, 146, 150, 153, 159, 167, 175, 185, 195, 204, 205, 
    211, 218, 226, 234, 237, 238, 240, 247, 254), c(0, 10, 10, 
    12, 13, 13, 13, 13, 13, 13, 13, 14, 46, 47, 47, 47, 47, 56, 
    62, 67, 71, 74, 76, 77, 83, 92, 105, 112, 124, 126, 131, 
    132, 132, 132, 132, 136, 139, 141, 142, 142, 144, 144, 153, 
    153, 153, 153, 153, 154, 155, 173, 178, 178, 182, 182, 182, 
    183, 192, 192, 200, 210, 217, 223, 228, 233, 237, 240, 242, 
    243, 243, 247, 250, 252, 253, 253, 254, 254, 254, 254), list(
        c(1, 0, 1), structure(list(), .Names = character(0)), 
        structure(list(id = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 
        11, 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), label = c("Myriel", 
        "Napoleon", "MlleBaptistine", "MmeMagloire", "CountessDeLo", 
        "Geborand", "Champtercier", "Cravatte", "Count", "OldMan", 
        "Labarre", "Valjean", "Marguerite", "MmeDeR", "Isabeau", 
        "Gervais", "Tholomyes", "Listolier", "Fameuil", "Blacheville", 
        "Favourite", "Dahlia", "Zephine", "Fantine", "MmeThenardier", 
        "Thenardier", "Cosette", "Javert", "Fauchelevent", "Bamatabois", 
        "Perpetue", "Simplice", "Scaufflaire", "Woman1", "Judge", 
        "Champmathieu", "Brevet", "Chenildieu", "Cochepaille", 
        "Pontmercy", "Boulatruelle", "Eponine", "Anzelma", "Woman2", 
        "MotherInnocent", "Gribier", "Jondrette", "MmeBurgon", 
        "Gavroche", "Gillenormand", "Magnon", "MlleGillenormand", 
        "MmePontmercy", "MlleVaubois", "LtGillenormand", "Marius", 
        "BaronessT", "Mabeuf", "Enjolras", "Combeferre", "Prouvaire", 
        "Feuilly", "Courfeyrac", "Bahorel", "Bossuet", "Joly", 
        "Grantaire", "MotherPlutarch", "Gueulemer", "Babet", 
        "Claquesous", "Montparnasse", "Toussaint", "Child1", 
        "Child2", "Brujon", "MmeHucheloup"), maincharacter = c(0, 
        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 
        0, 0, 0, 0, 1, 0, 1, 1, 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, 
        1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
        0, 0, 0, 0)), .Names = c("id", "label", "maincharacter"
        )), structure(list(value = c(1, 8, 10, 6, 1, 1, 1, 1, 
        2, 1, 1, 3, 3, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 3, 3, 
        3, 4, 3, 3, 3, 3, 5, 3, 3, 3, 3, 4, 4, 3, 3, 3, 3, 4, 
        4, 4, 2, 9, 2, 7, 13, 1, 12, 4, 31, 1, 1, 17, 5, 5, 1, 
        1, 8, 1, 1, 1, 2, 1, 2, 3, 2, 1, 1, 2, 1, 3, 2, 3, 3, 
        2, 2, 2, 2, 1, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 1, 1, 1, 
        2, 3, 2, 2, 1, 3, 1, 1, 3, 1, 2, 1, 2, 1, 1, 1, 3, 2, 
        1, 1, 9, 2, 2, 1, 1, 1, 2, 1, 1, 6, 12, 1, 1, 21, 19, 
        1, 2, 5, 4, 1, 1, 1, 1, 1, 7, 7, 6, 1, 4, 15, 5, 6, 2, 
        1, 4, 2, 2, 6, 2, 5, 1, 1, 9, 17, 13, 7, 2, 1, 6, 3, 
        5, 5, 6, 2, 4, 3, 2, 1, 5, 12, 5, 4, 10, 6, 2, 9, 1, 
        1, 5, 7, 3, 5, 5, 5, 2, 5, 1, 2, 3, 3, 1, 2, 2, 1, 1, 
        1, 1, 3, 5, 1, 1, 1, 1, 1, 6, 6, 1, 1, 2, 1, 1, 4, 4, 
        4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 2, 1, 1, 2, 
        2, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .Names = "value")), 
    "<environment>"), class = "igraph")

girvNew <- cluster_edge_betweenness(upgrade_graph(net))
dend <- as.dendrogram(girvNew )

library(dendextend)
# hopefully this is correct, but I'm not sure. It assumes that
# V(net)$label has the order of the original data
labels(dend) <- V(net)$label[order.dendrogram(dend)]

plot(dend)

library(colorspace)
k <- max(membership(girvNew))
colorsRainbow <- rainbow_hcl(k, alpha = 1) # [membership(girvNew)]

set.seed(23420)
colorsRainbow <- rainbow_hcl(max(membership(girvNew)))
colorsRainbow <- sample(colorsRainbow)
dend <- dend %>% set("labels_col", value = colorsRainbow, k = k) 
dend <- dend %>% set("branches_k_color", value = colorsRainbow, k = k) 

par(mar = c(3,1,1,5) )
plot(dend, horiz = T)

Выход:

А теперь с ggplot2:

library(ggplot2)
ggplot(dend) # the same as: ggplot(as.ggdend(dend))
# more work is needed for fixing the margins etc.

Обновленный код:

# dput(net)
net <- structure(list(16, FALSE, c(1, 2, 3, 2, 3, 3, 4, 5, 5, 7, 7, 
9, 8, 10, 9, 11, 11, 14, 15, 15, 15, 12, 14), c(0, 0, 0, 1, 2, 
1, 3, 3, 4, 3, 6, 6, 7, 8, 8, 8, 10, 11, 14, 13, 12, 3, 1), c(0, 
1, 3, 2, 5, 4, 6, 7, 8, 9, 10, 12, 11, 14, 13, 15, 16, 21, 22, 
17, 20, 19, 18), c(0, 1, 2, 3, 5, 22, 4, 6, 7, 9, 21, 8, 10, 
11, 12, 14, 13, 15, 16, 17, 20, 19, 18), c(0, 0, 1, 3, 6, 7, 
9, 9, 11, 12, 14, 15, 17, 18, 18, 20, 23), c(0, 3, 6, 7, 11, 
12, 12, 14, 15, 18, 18, 19, 20, 21, 22, 23, 23), list(c(1, 0, 
1), structure(list(), .Names = character(0)), structure(list(
    id = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 
    15), label = c("A", "B", "C", "D", "E", "F", "G", "H", "I", 
    "L", "M", "N", "O", "P", "Q", "R")), .Names = c("id", "label"
)), list()), "<environment>"), class = "igraph")


library(igraph)
net <- upgrade_graph(net)
# calculate degree
deg <- degree(net, mode = "all")

# find communities
com <- cluster_edge_betweenness(net) 
## or use 
# com <- fastgreedy.community(net)

# details on communities
com_sizesCom <- sizes(com) 
com_numCom <- length(com_sizesCom)


# create dendrogram
dend <- as.dendrogram(com)
plot(dend)
library(dendextend)
labels(dend) <- V(net)$label[order.dendrogram(dend)]
plot(dend)

k <- max(membership(com))
colorsRainbow <- rainbow(k, alpha = 1)

# colorsRainbow <- sample(colorsRainbow)
# dend <- rotate(dend, order(membership(comm)))
colorsRainbow <- rev(unique(colorsRainbow[membership(comm)[order.dendrogram(dend)]]))
dend <- dend %>% set("labels_col", value = colorsRainbow, k = k)
dend <- dend %>% set("branches_k_col", value = colorsRainbow, k = k)
dend <- dend %>% set("labels_cex", 1)
plot(dend)