ggtree
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YuLab-SMU
:christmas_tree:Visualization and annotation of phylogenetic trees
Hello Uncle Yu, Thank you and your team for bringing us such a powerful **ggtree** package. I'd like to ask if **ggtree** can achieve the following style of visualization, which...
I'm aligning a tree to a set of data points to show relationship over time. My data set has sample number in the first column (corresponding to tree) and date...
Hi, I have used RAxML EPA to place shorter reads of few OTUs onto a reference tree of longer sequences. My objective would be to obtain a tree incorporating the...
I try to colourize my TREE (Phylogenetic tree with 1846 tips and 1844 internal nodes.) by Phylum. I follow the exact steps outlined [here](https://yulab-smu.github.io/treedata-book/chapter6.html#group-taxa-vis) It runs smoothly for the example...
Hi. when I try to remove the bar as suggested by https://yulab-smu.top/treedata-book/chapter10.html a warning is emited. Alternatively, setting the barsize to zero also doesn't remove the bar. ``` > library(ggtree)...
Hi, rotate behaves peculiar, when rotating a node of a tree. ``` # data from tree book tree internal node number to specify a clade. If NULL, using the whole...
Hi, I have a problem plotting clade labels. They seem to oriented inverted, if I plot them using `angle = "auto"` ``` > library(ggtree) > library(ape) > x p p...
> install_zip("ggtree-master.zip") WARNING: Rtools is required to build R packages, but is not currently installed. Please download and install Rtools 4.0 from https://cran.r-project.org/bin/windows/Rtools/. √ checking for file 'C:\Users\wzz\AppData\Local\Temp\Rtmp4AGaZ1\file38144268d4\ggtree-master/DESCRIPTION' - preparing...
Hi, `geom_nodelab` reports an error, when using the `offset` argument. ``` > nwk tree td td$label # works > ggplot(tidytree::as.treedata(td), aes(x, y)) + geom_tree() + theme_tree() > # works >...
