Re: [igraph] subgraph by passing list of nodes that grabs also nodes pointing to that list

[Jose Quesada]

Gábor Csárdi wrote:

Thanks Gabor,
> there are many ways to do this, perhaps the simplest is to use
> neighborhood() to collect the neighboring vertices and then call
> subgraph().
>
> vv <- neighborhood(g, order=1, nodes=mynodes, mode="in")
>   
hmm, this doesn't work on my network; it returns exactly the same list,
mynodes, with no additional ones.
I created the network by reading from a MatrixMarket file into a
CsparseMatrix object with readMM, then constructing the graph from that
matrix.

I'm attaching a toy example, and code to reproduce the problem:

library(igraph)
library(Matrix)

# Toy: just last few movies
dataMtxFile = "movies2actors-10-idsOnly.mtx"
# ma for movie actors
matoy = as(readMM(paste(datapath, dataMtxFile, sep="")), "CsparseMatrix")
tg = graph.incidence(matoy, directed=T, mode="out")
mynodes =  1377253
vv <- neighborhood(tg, order=1, nodes=mynodes, mode="in")
vv
#> vv
#[[1]]
#[1] 1377253 <- lists only the original node; misses five inbound
connections.
vv <- neighborhood(tg, order=1, nodes=mynodes, mode="all") #same for out
vv # this lists all nodes but the ones that are actually connected to
1377253
# [[1]]
#  [1] 1377253 1413423 1457015 1464520 1517383 1641295 1704978 1741976
1744269 1744274 1744315 1745028 1745031 1756801 1783566
# [16] 1803739 1836911 1836953 1836954 1836964 1836967 1844560 1848929
1880207 1946456 2132881 2203538 2278148 2282809 2324406
# [31] 2409592 2409595 2410120 2410900 2681118 2946503 2946504 2946655
2974742

What am I doing wrong?

Thanks!
-Jose
> subgraph(g, unique(unlist(vv)))
>
> Best,
> Gabor
>   


-- 
Jose Quesada, PhD.
Max Planck Institute,
Center for Adaptive Behavior and Cognition -ABC-, 
Lentzeallee 94, office 224, 14195 Berlin
http://www.josequesada.name/           

%%MatrixMarket matrix coordinate real general           
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