Greg Rov - 2 months ago 15

R Question

I need to organize my results of correlation in a matrix, for example. I have a file like this:

`trait1 trait2 GeCor PCor`

a b -1.00 0.28

b c 0.40 0.45

d e -0.39 0.35

a c -0.39 0.50

b d 0.36 0.30

a d -0.35 0.30

b e -0.29 0.36

a e 0.26 0.33

c e 0.18 0.38

c d 0.04 0.31

And I need that file stay this way:

`a b c d e`

a - 0.28 0.50 0.30 0.33

b -1.00 - 0.45 0.30 0.36

c -0.39 0.40 - 0.31 0.38

d -0.35 0.36 0.04 - 0.35

e 0.26 -0.29 0.18 -0.39 -

The symbol on the diagonal (

`-`

`GeCor`

`trait1`

`trait2`

`PCor`

`trait1`

`trait2`

Answer

I think it is time to post my solution with R.

First, with `read.table`

, read in your original data into a data frame, say `x`

. Then

```
n <- ceiling(sqrt(2 * nrow(x)))
z <- matrix(NA, n, n, dimnames = list(letters[1:n],letters[1:n]))
z[lower.tri(z)] <- with(x, GeCor[order(trait1, trait2)])
z[upper.tri(z)] <- with(x, PCor[order(trait2, trait1)])
# a b c d e
#a NA 0.28 0.50 0.30 0.33
#b -1.00 NA 0.45 0.30 0.36
#c -0.39 0.40 NA 0.31 0.38
#d -0.35 0.36 0.04 NA 0.35
#e 0.26 -0.29 0.18 -0.39 NA
write.table(z, file = "z.txt" na = "-", sep = "\t", quote = FALSE)
## what the text file looks like
a b c d e
a - 0.28 0.5 0.3 0.33
b -1 - 0.45 0.3 0.36
c -0.39 0.4 - 0.31 0.38
d -0.35 0.36 0.04 - 0.35
e 0.26 -0.29 0.18 -0.39 -
```