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YuLab-SMU
:christmas_tree:Visualization and annotation of phylogenetic trees
Hi All, After importing codeml_tree from codon based alignment, I tried to add annotation of amino acid substitution inferred by joint probabilities with the following command: merged_tree
I really like what you have done here! Not sure if this is a bug or a feature request, but the flip and rotate functions don't seem to work well...
Hi, the inset feature is a great way of richly annotating trees but, in my opinion, it suffers from overlap of the annotations whenever a tree has a branch consisting...
When making an unrooted tree and flipping it using e.g. coord_flip() or visualized using ggplotify::as.ggplot(angle=-30, scale=.9) the angle of the labels aren't following the flip, but keeps the original angle....
I posted my problem on stack overflow and a user suggested that it was because of a bug. https://stackoverflow.com/questions/73517862/is-there-a-way-to-highlight-multiple-clades-of-an-unrooted-phylogenetic-tree-usi I want to plot an unrooted phylogenetic tree that neatly highlights...
### Prerequisites + [ ] Have you read [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [ ] make sure your are using the latest release version * [ ] read the...
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...
```r # Create two trees of different sizes; label nodes that aren't common to both. set.seed(0) lg
`rect_to_poly`在`geom_hilight`中有使用，，然而这个函数有问题，而且已经被`ggplot2`移除了，. 所以我们也需要对接一下，参考`ggplot2`中新的实现，因为老的实现如果直接搬过来的话，那问题依然存在，在使用极坐标时，形状有点问题。
I am generating a phylogenetic tree for 27 different fungi species, each species ieither has the trait "necrotrophic", "biotrophic" or "hemibiotrophic", i now want the species labels to be colored...
