Re: [igraph] "get.vertex.attribute(graph, name, index=V(graph))" ?

[Gábor Csárdi]

Local transitivity returns the results in the same order as the
vertices in `vids`. If this is what you are asking.

Gabor

On Mon, Jun 16, 2014 at 11:48 AM, Qunawei Zhang <address@hidden> wrote:
> Thanks.
> I just had a try following your suggestions. Based on the result, it seems
> that the "cc_seeds" are in the same order with "seedGenes"(which are
> described by gene symbols). Is this what you did in your code, or I just
> get such result by chance?
>
> So the question is:
> when a seedGene list is upload by "vids", will the output be in the same
> order as seedGenes? If so, will other functions report the result in the
> same way as the function "transitivity"?
>
> cc_seeds=transitivity(myNetwork,type="local",isolates="NaN",vids=seedGenes)
>
>
> Many thanks
>
> Best
> Quanwei
>
>
>
> On 6/16/14 10:52 AM, "Gábor Csárdi" <address@hidden> wrote:
>
>>I believe I answered this already:
>>
>>http://lists.nongnu.org/archive/html/igraph-help/2014-06/msg00039.html
>>
>>Gabor
>>
>>On Mon, Jun 16, 2014 at 10:49 AM, Qunawei Zhang <address@hidden>
>>wrote:
>>> Hello:
>>>
>>> I have a question about "get.vertex.attribute(graph, name,
>>>index=V(graph))".
>>> My network is protein-protein interaction network (suppose I save my
>>>network
>>> as "myNetwork").
>>> (1)By the following command, I can get all the genes in the network. Is
>>>the
>>> sequence in "allGenes" corresponding to node id in the network? That is,
>>> allGenes[1] --> node 1;  allGenes[2] --> node 2,Š,allGenes[i] --> node
>>>i ?
>>> allGenes=get.vertex.attribute(myNetwork,name="name")
>>>
>>> (2) I have some seed genes, which we are interested(noted as
>>>"seedGenes"). I
>>> calculated their clustering coefficient by the following command. But we
>>> can't see the gene symbol in the output (which is available when we
>>> calculate degrees). Is there some way we can map "cc_seeds" to
>>> "seedGenes"(I.e., gene symbols)?  I know we can calculate the clustering
>>> coefficient for each gene, separately. But I am afraid it will cost more
>>> time. Any suggestions?
>>>
>>>cc_seeds=transitivity(myNetwork,type="local",isolates="NaN",vids=seedGene
>>>s)
>>>
>>>
>>> Thanks
>>>
>>> Best
>>> Quanwei
>>>
>>>
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>>>
>>
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