Open barizona opened 1 year ago
I see this as well with ggtree 3.10.0
You can use the MAX_COUNT
parameter to reduce the amount of time the daylight algorithm takes. Basically, the algorithm starts with an equal angle layout and then perturbs the branches to get a better arrangement. MAX_COUNT
is the maximum number of iterations that the algorithm does (passes through each branch). The default is MAX_COUNT = 5
, but you can set it to MAX_COUNT = 1
to only do one iteration (this will result in a more equal angle like layout).
ggtree(tree, layout = 'daylight', MAX_COUNT = 1)
Also, the daylight layout is not really intended for trees with 1000s of tips.
Hi there!
I am also having trouble with the daylight visualization. My unrooted tree looks very ugly. However, it's just a typical unrooted tree:
Do you have any recommendations for how to improve the daylight visualization? I like the equal_angle but the tip labels end up being too close together so I wouldn't mind getting some more space between tips.
@dariotommasini Did you try using a small MAX_COUNT
(1 or 2)? The daylight algorithm works by rotating the branches away from an equal angle layout. It often overcompensates and the branches overlap.
ggtree(tree, layout = 'daylight', MAX_COUNT = 1)
Hi,
I use ggtree a lot and it seems like ggtree is unable to plot an unrooted (or daylight which is equivalent to unrooted) tree over 100 tips in a "normal" amount of time or even crash. I've checked it with random trees:
10 tips:
warning:
100 tips:
warning:
1000 tips:
warning:
In the case of _equalangle unrooted or rooted tree outputs processing time is not a problem:
Is it possible to improve this?
Best regards, Eszter
sessionInfo()