在R中使用igraph创建子图

Question

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)

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

DATABASE.ncol:

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

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

Answer 1

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)

Graph g1 :

Graph g2 :

Graph g3 :

Answer 2

There is a built-in igraph function for that. Try 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"))

Answer 3

How do we use a selected set of vertices based on an attribute that could be NA for some of the vertices? imagine in your example V(graph)$att1 <- c(1,2,NA,1,2,3,NA) and wanted to select the vertices that had att1 == 1. I tried selecting the name of those vertices by V(graph)[att1 == 1, na_ok = TRUE]$name but it doesn't work. gives me error "Error in if (is.numeric(v) && any(v < 0)) { : missing value where TRUE/FALSE needed"