matrix to vector

Hi,

   Is there a way to  convert a matrix into a vector representing all
permutations of values and column/row headings with native R functions?
I did this with 2 nested for loops and it took about 25 minutes to run
on a  ~700x700 matrix.  I'm assuming there must be a smarter way to do
this with R's vector commands, but being new to R, I'm having trouble
making it work. 

> cbind(expand.grid(rownames(x),colnames(x)),as.vector(x))
   Var1 Var2 as.vector(x)
1    d    a            1
2    e    a            2
3    f    a            3
4    d    b            4
5    e    b            5
6    f    b            6
7    d    c            7
8    e    c            8
9    f    c            9

 > x <- matrix(rnorm(700*700),700)
 > rownames(x) <- paste("R",1:700)
 > colnames(x) <- paste("C",1:700)
 > system.time(foo <- 
cbind(expand.grid(rownames(x),colnames(x)),as.vector(x)))
    user  system elapsed
   1.082   0.107   1.193

 

Thanks,

Ian

 

     [a] [b] [c]

[d]    1    4    7

[e]    2    5    8

[f]    3    6    9

 

a d 1

a e 2

a f 3

b d 4

b e 5

b f 6

c d 7

c e 8

c f 9

 

 

 

 

Ian Coe

 

Connective Capital Management, LLC

385 Homer Ave.

Palo Alto, CA 94301

(650) 321-4826 ext. 03     

 

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Not sure it is really "matrix to vector" but here are a few of attempts:

 > abM<-matrix(1:9, nrow=3)
 > rownames(abM) <- letters[1:3]
 > colnames(abM) <- letters[4:6]

 > data.frame( cols=colnames(abM)[col(abM)[1:9]], rows= rownames(abM) 
[row(abM)[1:9]], vals=abM[1:9])
   cols rows vals
1    d    a    1
2    d    b    2
3    d    c    3
4    e    a    4
5    e    b    5
6    e    c    6
7    f    a    7
8    f    b    8
9    f    c    9

 > matrix( c(colnames(abM)[col(abM)[1:9]], rownames(abM)[row(abM) 
[1:9]], abM[1:9]) ,ncol=3)
# all text values since matrices in R need to be of homogenous type
       [,1] [,2] [,3]
  [1,] "d"  "a"  "1"
  [2,] "d"  "b"  "2"
  [3,] "d"  "c"  "3"
  [4,] "e"  "a"  "4"
  [5,] "e"  "b"  "5"
  [6,] "e"  "c"  "6"
  [7,] "f"  "a"  "7"
  [8,] "f"  "b"  "8"
  [9,] "f"  "c"  "9"

But the most compact would be:

 >library(reshape)
 > melt(abM)
   X1 X2 value
1  a  d     1
2  b  d     2
3  c  d     3
4  a  e     4
5  b  e     5
6  c  e     6
7  a  f     7
8  b  f     8
9  c  f     9

Hi,

  Is there a way to  convert a matrix into a vector representing all
permutations of values and column/row headings with native R  
functions?
I did this with 2 nested for loops and it took about 25 minutes to run
on a  ~700x700 matrix.  I'm assuming there must be a smarter way to do
this with R's vector commands, but being new to R, I'm having trouble
making it work.

Thanks,

Ian


    [a] [b] [c]

[d]    1    4    7

[e]    2    5    8

[f]    3    6    9



a d 1

a e 2

a f 3

b d 4

b e 5

b f 6

c d 7

c e 8

c f 9
--
Ian Coe

Connective Capital Management, LLC

385 Homer Ave.

Palo Alto, CA 94301

(650) 321-4826 ext. 03

David Winsemius, MD
Heritage Laboratories
West Hartford, CT