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
Description. subgraph creates a subgraph of a graph, containing only the specified vertices and all the edges among them.
Subgraph. A graph in data structure is said to be a subgraph if it is a part of another graph. In the following example, graphs H1, H2 and H3 are subgraphs of the graph G.
ego_size calculates the size of the neighborhoods for the given vertices with the given order. ego calculates the neighborhoods of the given vertices with the given order parameter.
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 :
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"))
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