基于最大距离从距离矩阵中提取

Question

I have a distance matrix of genetic distances between pairs of isolates eg:

structure(c(0, 0.5, 0, 0.5, 0, 0.3, 0, 0.3, 0), .Dim = c(3L, 
3L), .Dimnames = list(c("A", "B", "C"), c("A", "B", "C")))

I have made a huge heatmap of ~ 5000 isolates but this is far to big to extract the interesting areas from by reading the labels and so I want to filter my distance matrix to get eg. all pairs of isolates with a distance < 0.5.

My output might look like:

B    C    0.3

How can I do this?

Answer 1

Something like this?

m <- structure(
  c(0, 0.5, 0, 0.5, 0, 0.3, 0, 0.3, 0),
  .Dim = c(3L,
           3L),
  .Dimnames = list(c("A", "B", "C"), c("A", "B", "C"))
)
# we convert matrix m to long format
m2 <-
  matrix(m, dimnames = list(t(outer(
    colnames(m), rownames(m), FUN = paste
  )), NULL))
# and finally we subset it
(vec <- m2[m2[, 1] < 0.5,])
#> A A A C B B B C C A C B C C 
#> 0.0 0.0 0.0 0.3 0.0 0.3 0.0