r - 用 igraph 在 R 中绘制相对较大的网络

Question

我有两个问题，第一个比第二个更复杂。

1. 我在下面有一张我的网络图，但是该图相当密集，如何将节点分散得更多，以便我可以清楚地看到边缘。我尝试了一个圆形情节，但我仍然得到了一个相当集中的情节。

2. 如何重命名节点？当前绘图在节点名称前放置了一个“X”，如何删除“X”？

在我的矩阵中，交互节点标记为1，非交互节点标记为0

代码：

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)

矩阵：

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

Answer 1

对于第一个问题，检查?igraph::layout. 有一些说明如何更改节点的对齐方式。

对于您的第二个问题，我猜该图从矩阵的行名或列名中获取节点的名称，但read.table默认情况下会附加带有前缀 X 的名称，以便使名称以数字有效的变量名称开头（请参阅 参考资料make.names）。所以你的矩阵的行名实际上是 X1、X2 等。你可以通过像这样读取你的矩阵来规避这个：

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

或者您可以在制作图表之前重命名矩阵的行和列，即

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

Answer 2

对于您问题的第二部分，我将为行名和列名创建一个单独的文件。导入后，您可以设置列名和行名。

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)