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HMP_tree raw data? availability

1

Hi, where can I find the following data: tree

MjelleLab

Error when trying to scale and collaps multiple clades on tree

4

Hi there, I'm trying to visualize a tree with multiple selected clades being scaled (condensed) and collapsed to save space for a publication figure. I've seen the issue also reported...

janstrauss1

Arcs representing orthogonal components of the branches in the circular layout look very coarsely segmented with some trees. The effect is obviously particularly pronounced closer to the root: ````R library(ggtree)...

alephreish

How to get the node number

1

Hi Dr. Yu, I am trying to annotate my tree in ggtree. Do you happen to know How I can get the node number? Is there a way to plot...

Ruiqi-CUB

Hello! Thank you for making a really great tool available. I was hoping that you all might be able to implement some explicit handing of [treetime](https://treetime.readthedocs.io/en/latest/) outputs. Treetime has found...

uee9

### Summary `DESCRIPTION` file has the following line: ``` Remotes: GuangchuangYu/treeio ``` This line forces tools like renv (or pak, I think) to gather the latest treeio from github.com, instead...

idavydov

Warnings generated by normal use of ggheatmap function

3

I am getting a lot of warnings from using the ggtree() and gheatmap() functions under normal use. My plots look fine, but I was concerned I was doing something wrong....

AlexSCFraser

error in facet_plot():invalid tbl_tree object. Missing column: parent,node.

1

Hi I encountered the following error when using facet_plot(): ``` map=read.table("map.txt", header=T, sep="\t", comment.char="") tree_all

Avamost1

Heatmap colors are showing transparent when alpha is not used

1

I want to represent the presence/absence matrix of the pangenome with the newick tree using gheatmap. I want presence in black and absence in white: ``` pangenome

ireneortega

Hi, I have been trying to graph my CAFE5 results analysis from the file base_clade_results.txt. I have tried the tree annotation with the use specified annotation and using the .txt...

rsandean