1
創建以這種方式使用ggdendro樹形圖的集羣：添加標籤，以樹狀圖和顏色
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)
我也得到： 
我的網絡是：
> 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")
我希望在垂直軸上有網絡節點的名稱，並且羣集線是相同的用cluster_edge_betweenness函數計算社區的顏色。
這真的，如果他們是豐富多彩不要緊：
- 節點（標籤）或
- 集羣的線條或
- 每個集羣的背景。
重要的是，我可以根據顏色區分羣集，就像我可以在第一個圖（使用圓節點）中所做的那樣。
我該怎麼辦？我搜索了互聯網，但我無法解決。 謝謝
我試圖按照這兩個兩條路：
- 按照this post
- 使用jlhoward響應dendextend package
我從一開始就問題的都。
（1）在響應中，df是數據幀，而我有一個列表（net），我不知道如何正確地轉換我的網絡中的數據幀像在該示例。 無論如何，如果我嘗試（剛玩）做rownames(df) <- V(net)$label我得到
錯誤
row.names<-.data.frame（*tmp*，值=值）：長度 'row.names' 不可接受
完全正確。但繪製的結果是這樣的： 
它不使用net網絡節點的標籤，但這些df網絡。在我看來，很奇怪。
（2）這是我做了什麼：
library(igraph)
library(GGally)
library(ggplot2)
library(ggdendro)
library(dendextend)
library(dendextendRcpp)
library(zoo)
# load dataset
net <- read.graph("./dataset/lesmiserables.gml", format = c("gml"))
deg <- igraph::degree(net, mode = "all")
comm <- fastgreedy.community(net)
comm_sizesComm <- sizes(comm)
comm_numComm <- length(comm_sizesComm)
comm_modularity <- modularity(comm)
# plot communities
colorsRainbow <- rainbow(max(membership(comm)), alpha = 0.6)
pdf(file = "./output/prova_comm2.pdf")
plot(net,
vertex.size = plotrix::rescale(deg, c(5, 16)),
vertex.color = colorsRainbow[membership(comm)],
vertex.frame.color = NA,
vertex.label.color = "black",
vertex.label.cex = 0.5,
vertex.size = 10,
edge.color = "#d8d8d8",
layout = layout.fruchterman.reingold,
edge.curved = FALSE)
dev.off()
# create dendrogram
dend <- as.dendrogram(comm)
cut <- comm_numComm
# change labels
dend <- dend %>% set("labels", V(net)$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()
我贏得成功改變標籤和它們上色。 但是這兩個圖形之間的顏色不匹配。我不明白這是一個情節或樹狀圖構造的問題。
說明： 在第一曲線（一個由點表示的節點），我有一個藍色的社區有節點{永久，芳汀，Anzelma，森普利斯，...}。在黃色社區中有Marius，Magnon，Cosette，...}。
如果現在我去看看第二個圖（樹狀圖），我看到女士二和Anzelma節點是在兩個不同的社區。 這似乎是一個巨大的問題，我不知道如何開始解決。
（3）我也試過：
ggd1 <- as.ggdend(dend)
ggplot(ggd1)
而且問題是一樣的（2）：社區不匹配。
我創建這個簡單的圖形：
> 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")
，然後我找到社區和樹狀圖：
# 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)$label[order.dendrogram(dend)]
k <- max(membership(com))
colorsRainbow <- rainbow(k, alpha = 1)
set.seed(23420)
colorsRainbow <- rainbow(max(membership(com)))
colorsRainbow <- sample(colorsRainbow)
dend <- dend %>% set("labels_col", value = colorsRainbow, k = k)
dend <- dend %>% set("branches_k_color", value = colorsRainbow, k = k)
dend <- dend %>% set("labels_cex", 1)
我得到： 
所以顏色不正確。
整個更新的代碼。現在切換藍色和綠色。
library(igraph)
library(dendextend)
library(colorspace)
net <- upgrade_graph(net)
# dput(net)
# calculate degree
deg <- igraph::degree(net, mode = "all")
# plot network
x11()
plot(net,
vertex.size = plotrix::rescale(deg, c(8, 22)),
vertex.color = "tomato",
vertex.frame.color = NA,
vertex.label.color = "black",
vertex.size = 10,
edge.color = "#d8d8d8",
layout = layout.fruchterman.reingold,
edge.curved = FALSE)
# find communities
com <- cluster_edge_betweenness(net)
# details on communities
com_sizesCom <- sizes(com)
com_numCom <- length(com_sizesCom)
print(com_numCom)
# plot communities
colorsRainbow <- rainbow(max(membership(com)), alpha = 0.6)
x11()
par(mar = c(1, 1, 1, 1))
plot(net,
vertex.size = plotrix::rescale(deg, c(8, 22)),
vertex.color = colorsRainbow[membership(com)],
vertex.frame.color = NA,
edge.color = "#d8d8d8",
vertex.label.color = "black",
layout = layout.fruchterman.reingold,
edge.curved = FALSE)
# create dendrogram
dend <- as.dendrogram(com)
labels(dend) <- V(net)$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)
你見過[dendextend包（https://cran.r-project.org/web/packages/dendextend/插圖/ introduction.html）。此外，一些彩色樹狀圖[這裏]（http://stackoverflow.com/questions/21474388/colorize-clusters-in-dendogram-with-ggplot2） –
嗨@marielle，你不能（容易地）添加顏色與ggdendro。這是dendextend包中ggdend對象的動機。 –
@SandyMuspratt謝謝，我編輯的主要信息，我希望你能幫助我。 – marielle