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