ggtree

ggtree copied to clipboard

Install issue

2

I switched to latest version of R recently. I'm now trying to run an old bit of code and can't seem to get "ggtree" to install. Here is the message...

osoyer

Color coding tips and branches

1

### Prerequisites + [x] 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 [documents](https://yulab-smu.github.io/treedata-book/)...

anzshahid

I produced a tree and added nodes to it: ``` library(ggtree) library(treeio) tree

xieduo7

Changed branch length(hclust)

1

Hello Thank you for your great tool. Now I am using gene expression to plot tree, and I find that the branch length aways to be same(First figure), I want...

mengchengyao

I am using clusterProfiler and the function compareCluster to compare 3 conditions using function "enrichGO". However the results contatin in the Description field, but the ID column contains valid GO...

Shankav

groupOTU adds an extra group called 0

2

### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://yulab-smu.github.io/treedata-book/) * [x]...

MarekGierlinski

problem_of_revts()

1

Hi, I am having a problem of plotting ancestral states on the tree and reversing the time scale at the same time. I use Revgadets to plot ancestral states in...

Hong-Wun

Expanded docs for geom_tiplab()

3

Given that tip labels will often be cut off (not fully visible) if one uses: ``` ggtree(tree, branch.length = 'none') + geom_tiplab() ``` ...with any labels larger than short numbers/letters...

nick-youngblut

I am plotting species interaction data with gheatmap and wondering if it is possible to align a second phylogeny to the x axis of the heatmap?

maxfarrell

Some `layout` options cause error in ggtree()

2

Some of the options for the `layout` argument in `ggtree::ggtree()` cause an error (session and package version info below). The options that cause error are: 'ape' 'slanted' 'radial' 'equal_angle' 'daylight'...

cmt2