Question

this is a simple enough question that I’m suprised I can’t find any reference to anyone having asked it before. It’s not the same as this, nor is it covered by this discussion.

I have a 4-d matrix (dimensions 16x10x15x39) with named dimnames (it’s what happens when you cast a dataframe from, e.g. a csv. You get to the names of the dimnames with names(dimnames(matrix)))

I then want to replace the columns (i.e. the first dimension) with fractions of the row total, so I do this:

matrix2 <- apply(matrix1, c(2,3,4), function(x){x/sum(x)})

But now names(dimnames(matrix2)) is blank for the first dimension. The other dimname names have been preserved.

So: how can I run apply over a matrix with named dimnames and keep the names of all the remaining dimensions?

A reproducable example

Here’s simple example of the problem. Just run the whole code and look at the last two lines.

x <- data.frame(
  name=c("bob","james","sarah","bob","james",
         "sarah","bob","james","sarah","bob",
         "james","sarah"),
  year=c("1995","1995","1995","1995","1995",
         "1995","2005","2005","2005","2005",
         "2005","2005"),
  sample_num=c("sample1","sample1","sample1",
               "sample2","sample2","sample2",
               "sample1","sample1","sample1",
               "sample2","sample2","sample2"),
  value=c(1,2,3,2,3,4,1,2,3,2,3,4)
  )
x <- cast(x, sample_num ~ name ~ year)
x_fractions <- apply(y,c(2,3),function(x){x / sum(x)})

names(dimnames(x))
names(dimnames(x_fractions))

Answer 1

I’m not quite sure what you’re looking for, but I think sweep function fits well for your goal. Try:

result <- sweep(test, c(2,3,4), colSums(test), FUN='/')

Where test is the array created by @user2068776. dimnames are preserved.

dimnames(result)
$a
[1] "a1" "a2"

$b
[1] "b1" "b2"

$c
[1] "c1" "c2"

$d
[1] "d1" "d2"