You want to change the order of levels in a factor based on values in the data.

Use reorder() with the factor that has levels to reorder, the values to base the reordering on, and a function that aggregates the values:

# Make a copy since we'll modify it
iss <- InsectSprays
iss$spray

 [1] A A A A A A A A A A A A B B B B B B B B B B B B C C C C C C C C C C C C D D
[39] D D D D D D D D D D E E E E E E E E E E E E F F F F F F F F F F F F
Levels: A B C D E F

iss$spray <- reorder(iss$spray, iss$count, FUN=mean)
iss$spray

 [1] A A A A A A A A A A A A B B B B B B B B B B B B C C C C C C C C C C C C D D
[39] D D D D D D D D D D E E E E E E E E E E E E F F F F F F F F F F F F
attr(,"scores")
        A         B         C         D         E         F
14.500000 15.333333  2.083333  4.916667  3.500000 16.666667
Levels: C E D A B F