R extension in C, setting matrix row/column names - c

Question

I'm writing an R package that manipulates Matrices in C. Currently, the matrices returned to R have numbers for the row/column names. I would rather assign my own row/column names when modifying the object in C.
I've googled around for about an hour, but haven't found a good solution yet. The closest I've found is dimnames, but I want to name each column, not just the two dimensions. The matrices get larger than 4x4, below is just a small example of what I want to do.
The number of rows is 4^x where X is the length of the row name
Current
[,1] [,2] [,3] [,4]
[1,] 0.20 0.00 0.00 0.80
[2,] 0.25 0.25 0.25 0.25
[3,] 0.25 0.25 0.25 0.25
[4,] 1.00 0.00 0.00 0.00
[5,] 0.20 0.00 0.00 0.80
[6,] 0.25 0.25 0.25 0.25
[7,] 0.25 0.25 0.25 0.25
[8,] 1.00 0.00 0.00 0.00
[9,] 0.20 0.00 0.00 0.80
[10,] 0.25 0.25 0.25 0.25
[11,] 0.25 0.25 0.25 0.25
[12,] 1.00 0.00 0.00 0.00
[13,] 0.20 0.00 0.00 0.80
[14,] 0.25 0.25 0.25 0.25
[15,] 0.25 0.25 0.25 0.25
[16,] 1.00 0.00 0.00 0.00
Desired
[A] [C] [G] [T]
[AA] 0.20 0.00 0.00 0.80
[AC] 0.25 0.25 0.25 0.25
[AG] 0.25 0.25 0.25 0.25
[AT] 1.00 0.00 0.00 0.00
[CA] 0.20 0.00 0.00 0.80
[CC] 0.25 0.25 0.25 0.25
[CG] 0.25 0.25 0.25 0.25
[CT] 1.00 0.00 0.00 0.00
[GA] 0.20 0.00 0.00 0.80
[GC] 0.25 0.25 0.25 0.25
[GG] 0.25 0.25 0.25 0.25
[GT] 1.00 0.00 0.00 0.00
[TA] 0.20 0.00 0.00 0.80
[TC] 0.25 0.25 0.25 0.25
[TG] 0.25 0.25 0.25 0.25
[TT] 1.00 0.00 0.00 0.00

Answer 1

If you are open to C++ instead of C, then Rcpp can make this a little easier. We just create a list object with rows and column names as we would in R, and assign that to the dimnames attribute of the matrix object:
R> library(inline) # to compile, link, load the code here
R> src <- '
+ Rcpp::NumericMatrix x(2,2);
+ x.fill(42); // or more interesting values
+ // C++0x can assign a set of values to a vector, but we use older standard
+ Rcpp::CharacterVector rows(2); rows[0] = "aa"; rows[1] = "bb";
+ Rcpp::CharacterVector cols(2); cols[0] = "AA"; cols[1] = "BB";
+ // now create an object "dimnms" as a list with rows and cols
+ Rcpp::List dimnms = Rcpp::List::create(rows, cols);
+ // and assign it
+ x.attr("dimnames") = dimnms;
+ return(x);
+ '
R> fun <- cxxfunction(signature(), body=src, plugin="Rcpp")
R> fun()
AA BB
aa 42 42
bb 42 42
R>
The actual assignment of the column and row names is so manual ... because the current C++ standard does not allow direct assignment of vectors at initialization, but that will change.
Edit: I just realized that I can of course use static create() method on the row and colnames too, which makes this a little easier and shorter still
R> src <- '
+ Rcpp::NumericMatrix x(2,2);
+ x.fill(42); // or more interesting values
+ Rcpp::List dimnms = // two vec. with static names
+ Rcpp::List::create(Rcpp::CharacterVector::create("cc", "dd"),
+ Rcpp::CharacterVector::create("ee", "ff"));
+ // and assign it
+ x.attr("dimnames") = dimnms;
+ return(x);
+ '
R> fun <- cxxfunction(signature(), body=src, plugin="Rcpp")
R> fun()
ee ff
cc 42 42
dd 42 42
R>
So we are down to three or four statements, no monkeying with PROTECT / UNPROTECT and no memory management.

Answer 2

As Jim said, this is much easier to do in R. I'm passing the names into the C function via the nam argument.
#include <Rinternals.h>
SEXP myMat(SEXP nam) {
/*PrintValue(nam);*/
SEXP ans, dimnames;
PROTECT(ans = allocMatrix(REALSXP, length(nam), length(nam)));
PROTECT(dimnames = allocVector(VECSXP, 2));
SET_VECTOR_ELT(dimnames, 0, nam);
SET_VECTOR_ELT(dimnames, 1, nam);
setAttrib(ans, R_DimNamesSymbol, dimnames);
UNPROTECT(2);
return(ans);
}
If you put that code in a file called myMat.c, you can test it via the line below. I'm using Ubuntu, so you will have to change myMat.so to myMat.dll if you're on Windows.
R CMD SHLIB myMat.c
Rscript -e 'dyn.load("myMat.so"); .Call("myMat", c("A","C","G","T"))'

Answer 3

The note above is instructive. The dimnames is a list with the same number of elements as dimensions of the dataset, where each element corresponds to the number elements along that dimension, i.e., list(c('a','c','g','t'), c('a','c','g','t')).
To set that in C, I would recommend:
PROTECT(dimnames = allocVector(VECSXP, 2));
PROTECT(rownames = allocVector(STRSXP, 4));
PROTECT(colnames = allocVector(STRSXP, 4));
setAttrib( ? , R_DimNamesSymbol, dimnames);
You'll have to then set the relevant rowname and colname elements. In general, this stuff is much easier to do in R.
jim