`which()` function for matrix indices

For your first question you need to also pass arr.ind= TRUE to which:

> which(m == 1, arr.ind = TRUE)
     row col
[1,]   3   1
[2,]   2   2
[3,]   1   3
[4,]   4   3

You cannot mix numeric and alpha in a matrix, but you can in a data.frame:

> indices <- data.frame(ind= which(m == 1, arr.ind=TRUE))
> indices$rnm <- rownames(m)[indices$ind.row]
> indices$cnm <- colnames(m)[indices$ind.col]
> indices
  ind.row ind.col rnm cnm
c       3       1   c   e
b       2       2   b   f
a       1       3   a   g
d       4       3   d   g