使用igraph在R中繪製比較大的網絡

Question

我有兩個問題，第一個比第二個更復雜。

1. 我有一個我的網絡下面的情節，但劇情是聚集在一起，我怎麼能擴散節點出更多，所以我可以清楚地看到邊緣。我試過了一個圓形的情節，但我仍然有一個相當集羣的情節。

2. 如何重命名節點？當前的圖表在節點名稱的前面放置了一個「X」，我該如何刪除'X'？

以我基質的相互作用節點標有1，非相互作用的節點都標有0

代碼：

library(igraph) 

df <- as.matrix(read.table("sig_pairs_matrix_for_r.txt")) 

g=graph.adjacency(df,mode="undirected",weighted=NULL,diag=FALSE) 
plot.igraph(g,vertex.label=V(g)$name) 

矩陣：

 4 6 7 8 12 13 15 17 22 23 25 26 27 29 30 31 34 35 36 43 44 47 48 52 53 56 57 59 63 66 67 70 96 99 122 166 168 172 174 176 180 181 191 192 193 220 222 224 225 226 236 249 253 256 258 266 267 277 296 
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12 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 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 0 0 0 0 0 0 0 
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Answer 1

對於第一個問題，請檢查?igraph::layout。有一些說明如何改變節點的對齊。

對於你的第二個問題，我猜想圖表從矩陣的行或列名稱中獲取節點的名稱，但read.table默認附加帶前綴X的名稱，以使名稱以數字有效變量名稱開頭（請參閱make.names）。所以，你的矩陣rownames實際上是X1，X2等，您可以通過閱讀你的矩陣這樣的規避這樣的：

df <- as.matrix(read.table("sig_pairs_matrix_for_r.txt",check.names=FALSE)) 

或者你也可以做圖形，即

之前重命名你的矩陣的行和列

#newnames is a vector containing the new names, such as c("a","b",...) 
rownames(df)<-colnames(df)<-newnames 

Answer 2

對於你的問題的第二部分，我會爲行列名創建一個單獨的文件。一旦導入，您可以設置列和行名稱。

temp = read.csv("adj_matrix.csv", sep=",",head=FALSE) 
adjmatrix <- as.matrix(temp) 

temprow = read.csv("rownames.csv", sep=",",head=FALSE) 
rowns <-as.matrix(temprow) 

tempcol = read.csv("colnames.csv", sep=",",head=FALSE) 
cols <-as.matrix(tempcol) 

rownames(adjmatrix)<- rows 
colnames(adjmatrix)<- cols 

g1 <- graph.adjacency(adjmatrix, mode=c("directed"), weighted=NULL, diag=TRUE) 
plot.igraph(g1)