[R] Help on comparing two matrices
Michael Kogan
michael.kogan at gmx.net
Tue Aug 25 15:53:39 CEST 2009
Gabor: Wow, that seems to be exactly what I need! Does it matter that
"my" incidence matrices represent neighborhood relations between
vertices and faces rather than between vertices and edges?
Steve: Yep, I realize that this package is exactly what I'm searching
for. :)
Gabor Grothendieck schrieb:
> They can be regarded as incidence matrices rather than adjacency
> matrices and in that case it follows:
>
> library(igraph)
>
> # incidence matrix to canonical edge list
> inc2canel <- function(m) {
> g <- graph.incidence(m)
> cp <- canonical.permutation(g)
> can <- permute.vertices(g, cp$labeling)
> el <- get.edgelist(can)
> el[ order(el[,1], el[,2]), ]
> }
>
> # test it out
>
> m1 <- matrix(c(0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 1,
> 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0,
> 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1), 7)
> m2 <- m1[7:1, 8:1]
> m3 <- m2; m3[1, ] <- 1
>
> identical(inc2canel(m1), inc2canel(m2)) # TRUE
> identical(inc2canel(m1), inc2canel(m3)) # FALSE
>
>
>
> On Sun, Aug 23, 2009 at 6:09 PM, Steve
> Lianoglou<mailinglist.honeypot at gmail.com> wrote:
>
>> Hi,
>>
>> On Sun, Aug 23, 2009 at 4:14 PM, Michael Kogan<michael.kogan at gmx.net> wrote:
>>
>>> Thanks for all the replies!
>>>
>>> Steve: I don't know whether my suggestion is a good one. I'm quite new to
>>> programming, have absolutely no experience and this was the only one I could
>>> think of. :-) I'm not sure whether I'm able to put your tips into practice,
>>> unfortunately I had no time for much reading today but I'll dive into it
>>> tomorrow.
>>>
>> Ok, yeah. I'm not sure what the best way to do this myself, I would at
>> first see if one could reduce these matrices by some principled manner
>> and then do a comparison, which might jump to:
>>
>>
>>> Ted: Wow, that's heavy reading. In fact the matrices that I need to compare
>>> are incidence matrices so I suppose it's exactly the thing I need, but I
>>> don't know if I have the basics knowledge to understand this paper within
>>> the next months.
>>>
>> Ted's sol'n. I haven't read the paper, but its title gives me an idea.
>> Perhaps you can assume the two matrices you are comparing are
>> adjacency matrices for a graph then use the igraph library to do a
>> graph isomorphism test between the two graphs represented by your
>> adjacency matrices and see if they are the same.
>>
>> This is probably not the most efficient (computationally) way to do
>> it, but it might be the quickest way out coding-wise.
>>
>> I see your original example isn't using square matrices, and an
>> adjacency matrix has to be square. Maybe you can pad your matrices
>> with zero rows or columns (depending on what's deficient) as an easy
>> way out.
>>
>> Just an idea.
>>
>> Of course, if David's solution is what you need, then no need to
>> bother with any of this.
>>
>> -steve
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>> | Memorial Sloan-Kettering Cancer Center
>> | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
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>>
>>
>
>
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