将Adjacency Matrix转换为Cytoscape的Edgelist（csv文件） [英] Convert Adjacency Matrix into Edgelist (csv file) for Cytoscape

问题描述

我在csv文件中有一个大（200列/行）邻接矩阵。这详细描述了个人之间的互动。我想把这个文件转换成一个edgelist，它可以手动完成，但会花费大量的时间。

I have a large (200 columns/rows) adjacency matrix in a csv file. This details interactions between individuals. I would like to convert this file into an edgelist, it can be done manually, but would take an enormous amount of time.

一小部分数据如下所示（第一个单元格是一个空格）：

A small subset of the data is shown below (the first cell is a space):

        A   B   C   
    A   0   0   1   
    B   0   0   1   
    C   1   0   0   

我想将其转换为：

    A  1  C
    B  1  C
    C  1  A

这只是示例数据。基本上我想要的是绘制这些节点如何交互，并从中绘制这些交互的网络。我试过下面的代码在R包PCIT但它返回一个错误：

This is just example data. Essentially what I want is to plot the how these nodes interact, and from it plot a network of these interactions. I have tried the following code in the R package PCIT but it returns an error:

    install.packages("PCIT")
    library(PCIT)
    input=read.csv('mouse.csv',header=TRUE,row.names=1,check.names=FALSE)
    setwd('/Users/Plosslab/Documents/PythonStuff')
    getEdgeList(input, rm.zero=TRUE)

我得到以下错误：

    Error in structure(.Internal(as.vector(x, "double")), Csingle = TRUE) : 
    (list) object cannot be coerced to type 'double'

推荐答案

获取数据：

m <- as.matrix(read.table(text="
     A   B   C   D
    A   0   0   0   1
    B   0   0   1   0
    C   1   0   0   1",
   header=TRUE))

w <- which(m==1,arr.ind=TRUE)
data.frame(r=rownames(m)[w[,"row"]],
           i=1,
           c=colnames(m)[w[,"col"]])
##   r i c
## 1 C 1 A
## 2 B 1 C
## 3 A 1 D
## 4 C 1 D

（您关心订单吗？ ..？）

(Do you care about the order ... ?)

PCIT 无论如何都是对称的，所以这可能是一个问题。

PCIT assumes symmetry anyway, so that might be a problem for you.

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