使用R中的igraph创建子图

Question

我需要使用igraph从图（g）中获取种子节点的子图（节点的输入列表; file.txt）和它们的第一个交互者（邻居）。不幸的是，我最终只得到子图中的一个节点，而不是所有其他节点和边缘（顶点）将它们链接起来。

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)

获取整个子网（包括节点和顶点）的任何建议？或者是否有其他功能可用于创建子图？

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，每行一个边。边由两个由制表符分隔的符号顶点名称定义：

file.txt的

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

Answer 1

我不确定完全理解你的问题，所以我创造了一个（希望）不言自明的例子：

# 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)

图表g1：

图表g2：

图表g3：

Answer 2

有一个内置的igraph功能。试试make_ego_graph（）：

library(igraph)
graph <- make_ring(7)
V(graph)$name <- c("A", "B", "C", "D", "E", "F", "G")

# Get the list of induced subgraphs
subgraph <- make_ego_graph(graph, order=1, c("A", "D", "F"))