用igraph绘制R中相对较大的网络

时间：2013-03-08 15:00:52

标签： r igraph

我有两个问题，第一个问题比第二个问题复杂。

  1. 我在下面有一个我的网络图，但是该图是相当聚集的，我怎样才能将节点扩展出来以便我可以清楚地看到边缘。我尝试了一个圆形的情节，但我仍然有一个相当聚集的情节。

  2. 如何重命名节点？当前图表在节点名称前面放置一个“X”，如何删除“X”？

    3. 在我的矩阵中，交互节点标有1，非交互节点标有0

    enter image description here

    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

2 个答案:

答案 0 :(得分：2)

对于第一个问题，请检查?igraph::layout。有一些说明如何改变节点的对齐方式。

对于第二个问题，我猜图表从矩阵的行名或列名中获取节点的名称，但默认情况下read.table附加带有前缀X的名称，以便使名称以数字有效变量开头名称（见make.names）。因此矩阵的rownames实际上是X1，X2等。您可以通过读取这样的矩阵来避免这种情况：

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

或者你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

答案 1 :(得分：0)

对于问题的第二部分，我将为行名和列名创建单独的文件。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)
相关问题
最新问题