Creating Subgraph using igraph in R

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 AR…

Accepted Answer

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 :

Creating Subgraph using igraph in R

Solution

Problem