On 2020-06-11 14:54, Ana Marija wrote:
Hello,

I expected it to look like this:
https://imgur.com/a/pj40c


Ah - so all on the one plot? - so you don't want a facet. It puts two plots side by side (or 22)

where x-axis would be CHR, there is 22 of them
unique(tmp.tidy$CHR)
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22


You have 22 plots all appearing side by size as part of the facet

I think you want color=CHR - but I don't know what your current color setting is doing.

I also have two phenotypes (keys) which I would like to compare
unique(tmp.tidy$key)
[1] "Pold" "Pnew"


So did you want to Facet those?

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