Extract one triangle of a correlation matrix with attributes

Question

I have a dataframe/matrix of equal rows and columns. I want to extract only the upper or lower triangle.

x<-data.frame(matrix(1:25,nrow=5))
colnames(x)<-LETTERS[1:5]
rownames(x)<-LETTERS[1:5]

x[upper.tri(x,diag=F)]

From this result, it is not possible to say what combination of column and row the value came from. So, I would like to have the row and column attributes in the results. Something like this:

Col Row Val
B   A   6
C   A   11
C   B   12
...

I need to do this for a large correlation matrix. Thanks.

Answer 1

I'd just use which with arr.ind = TRUE like this:

ind <- which( upper.tri(x,diag=F) , arr.ind = TRUE )

data.frame( col = dimnames(x)[[2]][ind[,2]] ,
            row = dimnames(x)[[1]][ind[,1]] ,
            val = x[ ind ] )

   col row val
1    B   A   6
2    C   A  11
3    C   B  12
4    D   A  16
5    D   B  17
6    D   C  18
7    E   A  21
8    E   B  22
9    E   C  23
10   E   D  24

Answer 2

First, to make things unambiguous, I change

colnames(x) <- LETTERS[6:10]

Use expand.grid to get the row and column names like this

rowCol <- expand.grid(rownames(x), colnames(x))

To get the correct rows from this data frame, take

labs <- rowCol[as.vector(upper.tri(x,diag=F)),]
df <- cbind(labs, x[upper.tri(x,diag=F)])
colnames(df) <- c("Row","Col","Val")
df[,c(2,1,3)]
##    Col Row Val
## 6    G   A   6
## 11   H   A  11
## ...

Answer 3

... this might be a solution

nam <-apply(ind, 2, function(y, x) rownames(x)[c(y)], x=x)   
cbind(nam, x[upper.tri(x,diag=F)])

hth