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Hi Guangchuang,
I was trying to use the unrooted layouts in ggtree and I found that my trees always came out looking squished. Looking in the code I noticed that in
ggtree
function a yscale is added to the plot expanding the yscale by 0.6, which is more than my tree's length. Hence, I changed theggtree
function to use "coord_fixed` instead to plot with an 1:1 aspect ratio, which I think make more sense as a default.I also wrote in ape's unrooted layout. Though I didn't make it work with variable
branch.length
s yet.I put these changes in separate commits in case you don't want the ape layout.