Re: [igraph] Shortest path matrix

[seema aswani]

Hi all,

Is there any way in igraph package that if once i find the shortest path between two nodes using get.shortest.paths. Like for example

get.shortest.paths(g, 5 , 2) will return 5 4 3 2. Then if i just want to find the intermediate nodes except this two nodes 5 and 2..??

As a result i want to print the sequence 4 3 2.

Thank you.

On Mon, Jul 6, 2015 at 2:35 PM, Gábor Csárdi <address@hidden> wrote:

It is in igraph 1.0.0. If you want sg that works with older versions
as well, then you can use the 'name' vertex attribute. E.g.

library(igraph)
g <- graph.ring(10)
V(g)$name <- LETTERS[1:10]
sp <- get.shortest.paths(g, 'A', 'B')
V(g)[ sp$vpath[[1]] ]$name

This probably works with version 0.7.x as well, but I haven't actually
tried, sorry.

Gabor

On Mon, Jul 6, 2015 at 9:38 AM, seema aswani <address@hidden> wrote:
> Can you give any examle..??
>
> On Mon, Jul 6, 2015 at 1:04 PM, seema aswani <address@hidden> wrote:
>>
>> Hi ,
>> Thank you for you reply.
>> Is this  `as_ids` is inbuilt function in r?? I didn't found any..
>>
>> On Mon, Jul 6, 2015 at 12:49 PM, Gábor Csárdi <address@hidden>
>> wrote:
>>>
>>> "You can convert an igraph.vs to vertex names with `as_ids`, and
>>> vertex ids with `as.vector`."
>>>
>>> Gabor
>>>
>>> On Mon, Jul 6, 2015 at 9:10 AM, seema aswani <address@hidden>
>>> wrote:
>>> > Hi all,
>>> >
>>> > I want the matrix not with numbers but with the vertex names as protein
>>> > names. I already got the result of pair wise shortest path with its
>>> > vertex
>>> > names.
>>> > its class is igraph.vs. Is there any way to convert igraph.vs class in
>>> > to
>>> > matrix..??
>>> > a matrix like
>>> >
>>> >   [,1]                           [,2]
>>> > [1,] "trpA" "tprB"    "trpC"  trpD"
>>> >
>>> > That shows as result
>>> >
>>> >   [,1]      [,2]
>>> > [1,] String,2 String,2
>>> >
>>> > Thanks.
>>> >
>>> >
>>> >
>>> > On Sun, Jul 5, 2015 at 8:16 PM, seema aswani <address@hidden>
>>> > wrote:
>>> >>
>>> >> Hi Gabor,
>>> >> Thanks a lot for your response..:) It really helps alot.
>>> >>
>>> >> On Sun, Jul 5, 2015 at 7:59 PM, Gábor Csárdi <address@hidden>
>>> >> wrote:
>>> >>>
>>> >>> On Sun, Jul 5, 2015 at 4:18 PM, seema aswani <address@hidden>
>>> >>> wrote:
>>> >>>>
>>> >>>> Hi,
>>> >>>> Just tried the way you told. But it is giving the resultant matrix
>>> >>>> in
>>> >>>> form of
>>> >>>>     [,1]      [,2]
>>> >>>> [1,] Integer,3 Integer,3
>>> >>>> [2,] Integer,3 Integer,3 in your example. This is not giving the
>>> >>>> result
>>> >>>> as 1 2 3  1 2 3  3 2 1  3 2 1 as this.
>>> >>>
>>> >>>
>>> >>> Yes, you need to index the matrix to see the actual result. Lists can
>>> >>> contain pretty much any R object, so when your matrix has lists as
>>> >>> cells, R
>>> >>> cannot really print the contents, there is no guarantee that it would
>>> >>> even
>>> >>> fit to the screen.
>>> >>>
>>> >>> G.
>>> >>>
>>> >>> _______________________________________________
>>> >>> igraph-help mailing list
>>> >>> address@hidden
>>> >>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>> >>>
>>> >>
>>> >
>>> >
>>> > _______________________________________________
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>>> >
>>>
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>>
>>
>
>
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