Convert and save distance matrix to a specific format

Question

I got a distance matrix with the following steps:

x <- read.table(textConnection(\'
     t0 t1 t2
 aaa  0  1  0
 bbb  1  0  1
 ccc  1  1  1
 ffffd  1  1  0
         


        

Answer 1

you can do this by combining melt from reshape package, upper.tri etc.:

> library(reshape)
> m <- as.matrix(d)
> m
          aaa       bbb       ccc       ffffd
aaa 0.0000000 1.0000000 0.6666667 0.5000000
bbb 1.0000000 0.0000000 0.3333333 0.6666667
ccc 0.6666667 0.3333333 0.0000000 0.3333333
ffffd 0.5000000 0.6666667 0.3333333 0.0000000
> m2 <- melt(m)[melt(upper.tri(m))$value,]
> names(m2) <- c("c1", "c2", "distance")
> m2
    c1  c2  distance
5  aaa bbb 1.0000000
9  aaa ccc 0.6666667
10 bbb ccc 0.3333333
13 aaa ffffd 0.5000000
14 bbb ffffd 0.6666667
15 ccc ffffd 0.3333333

Answer 2

This is quite doable using base R functions. First we want all pairwise combinations of the rows to fill the columns c1 and c2 in the resulting object. The final column distance is achieved by simply converting the "dist" object d into a numeric vector (it already is a vector but of a different class).

The first step is done using combn(rownames(x), 2) and the second step via as.numeric(d):

m <- data.frame(t(combn(rownames(x),2)), as.numeric(d))
names(m) <- c("c1", "c2", "distance")

Which gives:

> m
   c1  c2  distance
1 aaa bbb 1.0000000
2 aaa ccc 0.6666667
3 aaa ffffd 0.5000000
4 bbb ccc 0.3333333
5 bbb ffffd 0.6666667
6 ccc ffffd 0.3333333

To save as a CSV file, write.csv(m, file = "filename.csv").