ggtreeextra and root length settings

[Antoine]

Good morning

First of all , thank you for this amazing workI have been using ggtree for a long time now and I have  a couple of questions

#1. First real quick: I can’t find the data to reproduce Fig10.2 from ggtree extra

https://yulab-smu.top/treedata-book/chapter10.html

can you redirect me to the github page or share the link. I have similar data to analyze but I would like to start from this example  to make sure everything is properly formatted

#2. This is more a problem I have been struggling with for some time now . it has to do with the root length and fan tree (and also how to position the scale and labels)

For example:

mytree <- mytree +   xlab("Subst./site")+  xlim(-0.01, NA)+  geom_treescale(x=0, y=0,  fontsize=16, linesize=4, offset=2,width=0.01)

 

clearly the scale bar, the legend and the root length are not ideal. Is there a comprehensive way to adjust these parameters? What if I have to loop over multiple tree files with different branch lengths?

 

[xshua...@163.com]

1. The dataset is aviable from https://github.com/YuLab-SMU/treedata-book/tree/master/data/HMP_tree

2. the x and y of geom_treescale control the postion of scale. I think you can set smaller fontsize and linesize.  

    The Fig10.2 of ggtreeExtra also has added geom_treescale layer, you can refer it.

[Antoine]

I was able to access the data, thank you!

when running the code for fig 10.2 

https://yulab-smu.top/treedata-book/chapter10.html

I got this error

``

 p <- ggtree(tree, layout="fan", size=0.15, open.angle=5) +

+         geom_hilight(data=nodedf, mapping=aes(node=node),

+                      extendto=6.8, alpha=0.3, fill="grey", color="grey50",

+                      size=0.05) +

+         geom_cladelab(data=labdf, 

+                       mapping=aes(node=node, 

+                                   label=label,

+                                   offset.text=pos),

+                       hjust=0.5,

+                       angle="auto",

+                       barsize=NA,

+                       horizontal=FALSE, 

+                       fontsize=1.4,

+                       fontface="italic"

+         )

Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale.

Error in structure(list(node = node, fill = fill, alpha = alpha, extend = extend,  : 

  argument "node" is missing, with no default

``

I copied/pasted the entire code and did not get error messages upfront.

thank you!

[xshua...@163.com]

please update ggtree to lastest version.

the geom_hilight and geom_cladelab of the newest ggtree have supported aesthetic mapping.