[BioC] [R] function to find coodinates in an array

[Marc Schwartz]

If I am correctly understanding the problem, I think that this is what
you want:

set.seed(1)

# Create a 3x3x3 array
ARR <- array(sample(100, 27), c(3, 3, 3))

> ARR
, , 1

     [,1] [,2] [,3]
[1,]   27   89   97
[2,]   37   20   62
[3,]   57   86   58

, , 2

     [,1] [,2] [,3]
[1,]    6   61   43
[2,]   19   34   88
[3,]   16   67   83

, , 3

     [,1] [,2] [,3]
[1,]   32   17   21
[2,]   63   51   29
[3,]   75   10    1


# Get the ordered indices of the elements in the array
> order(ARR)
 [1] 27 10 24 12 22 11  5 25  1 26 19 14  2 16 23  3  9 13  8 20 15 21
[23] 18  6 17  4  7


# Get the actual array elements in order
> ARR[order(ARR)]
 [1]  1  6 10 16 17 19 20 21 27 29 32 34 37 43 51 57 58 61 62 63 67 75
[23] 83 86 88 89 97


# Now loop over the above and using which(), get the 3D indices
> t(sapply(ARR[order(ARR)], function(x) which(ARR == x, arr.ind = TRUE)))
      [,1] [,2] [,3]
 [1,]    3    3    3
 [2,]    1    1    2
 [3,]    3    2    3
 [4,]    3    1    2
 [5,]    1    2    3
 [6,]    2    1    2
 [7,]    2    2    1
 [8,]    1    3    3
 [9,]    1    1    1
[10,]    2    3    3
[11,]    1    1    3
[12,]    2    2    2
[13,]    2    1    1
[14,]    1    3    2
[15,]    2    2    3
[16,]    3    1    1
[17,]    3    3    1
[18,]    1    2    2
[19,]    2    3    1
[20,]    2    1    3
[21,]    3    2    2
[22,]    3    1    3
[23,]    3    3    2
[24,]    3    2    1
[25,]    2    3    2
[26,]    1    2    1
[27,]    1    3    1


See ?which and take note of the arr.ind argument.

HTH,

Marc Schwartz


On Thu, 2007-08-16 at 19:21 -0700, Moshe Olshansky wrote:
> A not very good solution is as below:
> 
> If your array's dimensions were KxMxN and the "linear"
> index is i then
> n <- ceiling(i/(K*M))
> i1 <- i - (n-1)*(K*M)
> m <- ceiling(i1/K)
> k <- i1 - (m-1)*K
> 
> and your index is (k,m,n)
> 
> I am almost sure that there is a function in R which
> does this (it exists in Matlab).
> 
> Regards,
> 
> Moshe.
> 
> --- Ana Conesa <aconesa at ochoa.fib.es> wrote:
> 
> > Dear list,
> > 
> > I am looking for a function/way to get the array
> > coordinates of given
> > elements in an array. What I mean is the following:
> > - Let X be a 3D array
> > - I find the ordering of the elements of X by ord <-
> > order(X) (this
> > returns me a vector)
> > - I now want to find the x,y,z coordinates of each
> > element of ord
> > 
> > Can anyone help me?
> > 
> > Thanks!
> > 
> > Ana
> >