Re: [igraph] subsetting by vertex ids and keep all edges

I am sorry. I try it again.
I wish to subset a graph by an arry of vertex ids ( in my example this is zu). My subset should comprise my vertices of interest (zu) and the next neighouring vertices.

Example:

a-----b-----c------d-------e

| |

f g

vertices of interest: c and d

I get: b-c-d-e
|

Typing

induced.subgraph (g, zu)

generates a graph with the vertices (of zu) and with edges only between the (subsetted) vertices (of zu). I want a subset that includes the vertices (of zu) and all the edges of the vertices (of zu) and the corresponding vertices.

I tried:
idx <- unique (as.vector (g[zu, edges=TRUE])) # get edges ids for vertices of interest
idx <- idx[-1] # remove 0
ggzu <- subgraph.edges (g, idx)

And the results are okay but I guess its is very clumsy.

Thanks

dput (ggzu)
structure(list(3, FALSE, c(1, 2, 2), c(0, 0, 1), c(0, 1, 2),
    c(0, 1, 2), c(0, 0, 1, 3), c(0, 2, 3, 3), list(c(1, 0, 1),
        structure(list(), .Names = character(0)), structure(list(
            name = c("16052513", "16052618", "rs3013006"), x = c(16052513L,
            16052618L, 16054667L), y = c(2.547104, 1.587586,
            1.543943)), .Names = c("name", "x", "y")), structure(list(
            weight = c(0.725426, 0.681783, 0.86216), color = c("blue",
            "grey", "red")), .Names = c("weight", "color")))), class = "igraph")

2014-02-04 Gábor Csárdi <address@hidden>:

Hi, to be honest I have no idea what you want. Can you give a small example? E.g. what is the expected output of your example graph?

Gabor

On Tue, Feb 4, 2014 at 1:51 PM, Hermann Norpois <address@hidden> wrote:

Hello,

I have an igraph object g and I want to subset g by using vertex ids, for instance by

zu
[1] "16052618" "rs3013006".

I want to keep all edges of each defined vertix, also the edges my vertices share with other vertices. So induced.subgraph is not an option, isn't it?

I tried subgraph.edges but I guess my approach is very clumsy. So I ask for an amelioration.

I tried:

idx <- unique (as.vector (g[zu, edges=TRUE])) # get edges ids for vertices of interest
idx <- idx[-1] # remove 0
ggzu <- subgraph.edges (g, idx)

Do you have any suggestions?
Thanks
Hermann

dput (g)
structure(list(9, FALSE, c(6, 2, 7, 8, 7, 5), c(0, 1, 1, 1, 2,
3), c(1, 5, 0, 2, 4, 3), c(0, 1, 2, 3, 4, 5), c(0, 0, 0, 1, 1,
1, 2, 3, 5, 6), c(0, 1, 4, 5, 6, 6, 6, 6, 6, 6), list(c(1, 0,
1), structure(list(), .Names = character(0)), structure(list(
    name = c("16052361", "16052513", "16052618", "16052962",
    "rs11703994", "rs62224614", "rs78724352", "rs3013006", "rs55926024"
    ), x = c(16052361L, 16052513L, 16052618L, 16052962L, 16053791L,
    16053862L, 16053863L, 16054667L, 16054740L), y = c(2.156147,
    2.547104, 1.587586, 4.037532, 3.734964, 5.026869, 2.514876,
    1.543943, 0.579408)), .Names = c("name", "x", "y")), structure(list(
    weight = c(0.526203, 0.725426, 0.681783, 0.579408, 0.86216,
    0.718093), color = c("grey", "blue", "grey", "grey", "red",
    "blue")), .Names = c("weight", "color")))), class = "igraph")

    dput (zu)
c("16052618", "rs3013006")

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From:	Hermann Norpois
Subject:	Re: [igraph] subsetting by vertex ids and keep all edges
Date:	Wed, 5 Feb 2014 13:36:15 +0100