Subsetting matrices of different dimensions

Question

Let's say I have two similarity matrices of different dimensions and with some of their row.names in common but not in the same order, such as:

> m1
            red   yellow     blue    green    black
red    0.000000 2.236068 4.472136 6.708204 8.944272
yellow 2.236068 0.000000 2.236068 4.472136 6.708204
blue   4.472136 2.236068 0.000000 2.236068 4.472136
green  6.708204 4.472136 2.236068 0.000000 2.236068
black  8.944272 6.708204 4.472136 2.236068 0.000000

> m2
         purple    green     blue     red
purple 0.000000 0.081172 4.472136 6.708204
green  0.081172 0.000000 0.107647 4.472136
blue   4.472136 0.107647 0.000000 0.073217
red    6.708204 4.472136 0.073217 0.000000

I want to subset m1 to a new matrix that only contains the rows in common with m2. The final result should look like:

> m3
            red      blue    green    
red    0.000000  4.472136 6.708204 
blue   4.472136  0.000000 2.236068 
green  6.708204  2.236068 0.000000 

Note that in the "real" data, the matrices are hundreds of dimensions. The subset command seems to be for subsetting data in reference to itself, not in reference to other data frames or matrices? Anyway I tried creating an index of the matches like so:

index <- m1 %in% m2 

which is fine, but I get an error when trying to transform this object into a new matrix using cbind or a for loop. I know there must be a reasonably quick or elegant way to do this, but documentation seems a bit terse on this subject. Ideally after transforming m1 to m3, I want to perform some basic arithmetic operations on the values in the matching elements of m2 and m3 such as m2(2,3) - m3(3,2) = -2.128421. Hope this makes sense.

Many thanks in advance!!

Answer 1

  m3<-m1[row.names(m1) %in% row.names(m2),]
               red   yellow     blue    green    black
    red   0.000000 2.236068 4.472136 6.708204 8.944272
    blue  4.472136 2.236068 0.000000 2.236068 4.472136
    green 6.708204 4.472136 2.236068 0.000000 2.236068


     m3[,rownames(m3)]
           red     blue    green
red   0.000000 4.472136 6.708204
blue  4.472136 0.000000 2.236068
green 6.708204 2.236068 0.000000

Answer 2

Try something like merge(m1,m2,all.x=FALSE,all.y=TRUE,by="colorrow"). First have to take the rownames of each matrix into a column named colorrow.