在R中使用igraph创建子图 [英] Creating Subgraph using igraph in R

问题描述

我需要使用igraph从图(g)获取种子节点(节点的输入列表； file.txt)及其第一个交互器(邻居)的子图.不幸的是，我最终仅在子图中得到一个节点，而不是所有其他将它们互连的节点和边(顶点).

I need to obtain a subgraph of the seed nodes (the input list of nodes; file.txt) and their first interactors (neighbours) from a graph (g) using igraph. Unfortunately, I am ending up with only a single node in the subgraph, and not all the rest of the nodes and edges (vertices) which interlink them.

g<-read.graph("DATABASE.ncol",format="ncol",directed=FALSE) #load the data
g2<-simplify(g, remove.multiple=TRUE, remove.loops=TRUE) # Remove the self-loops in the data
DAT1 <- readLines("file.txt")   #It provides a character vector right away
list_nodes_1 = neighbors(g2, DAT1) #list of nodes to be fetched in subnetwork
list_nodes_1 # 16
g3 <- induced.subgraph(graph=g2,vids=DAT1) #subnetwork construction
g3 # GRAPH UN-- 1 0 --; indicating only one node
plot (g3)

对获得整个子网(包括节点和顶点)有何建议?还是有其他功能可用于创建子图?

Any suggestions for obtaining the whole subnetwork (including nodes and vertices)? or is there any other function available for creating sub-graphs?

DATABASE.n​​col:

MAP2K4  FLNC
MYPN    ACTN2
ACVR1   FNTA
GATA2   PML
RPA2    STAT3
ARF1    GGA3
ARF3    ARFIP2
ARF3    ARFIP1
XRN1    ALDOA
APP     APPBP2
APLP1   DAB1
CITED2  TFAP2A
EP300   TFAP2A
APOB    MTTP
ARRB2   RALGDS
CSF1R   GRB2
PRRC2A  GRB2
LSM1    NARS
SLC4A1  SLC4A1AP
BCL3    BARD1

这是一个简单的文本文件，每行一条边.边缘由两个用制表符分隔的符号顶点名称定义:

It is a simple text file with one edge per line. An edge is defined by two symbolic vertex names delimited by tab:

file.txt

ALDOA
APLP1
GRB2
RPA2
FLNC
BCL3
APP
RALGDS
PRRC2A
NARS
LSM1
GGA3
FNTA

推荐答案

我不确定是否完全了解您的问题，所以我创建了一个(希望)不言自明的示例:

I'm not sure to have completely understood your problem, so I have created a (hopefully) self-explanatory example:

# for example reproducibility
set.seed(123)

# create a fake undirected graph
D <- read.table(
sep=',',
header=T,
text=
'from,to
A,B
A,C
D,E
F,G
H,I')

g1 <- graph.data.frame(D,directed=F)
plot(g1)

# we want a sub-network containing the floowing nodes:
subv <- c('A','B','H')

# first method: 
# create a sub-network composed by ONLY the nodes in subv and the edges 
# between them
g2 <- induced.subgraph(graph=g1,vids=subv)
plot(g2)

# second method: 
# create a sub-network composed by the nodes in subv and, if some of them is
# connected to other nodes (even if not in subv), take also them 
# (and of course include all the edges among this bunch of nodes). 
sg1 <- decompose.graph(g1,mode="weak")
neighverts <- unique(unlist(sapply(sg1,FUN=function(s){if(any(V(s)$name %in% subv)) V(s)$name else NULL})))
g3 <- induced.subgraph(graph=g1,vids=neighverts)
plot(g3)

图形g1:

图形g2:

图形g3:

这篇关于在R中使用igraph创建子图的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！