Formatting tip labels with different fonts

[Frederik Bak]

Hi, 

I am trying to plot a tree where some of the tip labels are supposed to be bold and some are to be italic. 

I have read this: https://guangchuangyu.github.io/ggtree/faq/#formatting-tip-labels but it is still a bit unclear to me. 

I have thought about two ways to do it. One is: 

ggtree(phyloseqobject)+  geom_tiplab(aes(label=Name), align = TRUE, linetype = 0, offset = 0.04) + geom_text2(aes(label = label, fontface = "italic", subset=node %in% Mylist))+geom_text2(aes(label=label, fontface = "bold", subset = node %in% Mylist2))

Obviously, this plots the label names twice. I could off course skip the geom_tiplab part, but I really like the alignment which is made here. 

Another way could be something like:

I have not included the bold part in this one, but I assume it would just be adding another "+geom_tiplab(xxx)" afterwards?

ggtree(phyloseqobject) +  geom_tiplab(aes(subset = node %in% Mylist),label=substitute(italic(x),list(x=c(1:20)[1])), parse=T, align = TRUE, linetype = 0, offset = 0.04)

Here I get this error:

Warning: Ignoring unknown parameters: label, parse

Error: Aesthetics must be either length 1 or the same as the data (20): label, hjust

Mylist has the length 20 which is why I wrote c(1:20) (could has well been a vector with 20 labels). I do not know why this error occurs.

I think the latter option is the preferable one, in order to keep the alignment, but I need to be able to overcome the error.

Frederik

[Yu, Guangchuang]

​

--
G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
 
Homepage: https://guangchuangyu.github.io/ggtree
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--

--~--~---------~--~----~------------~-------~--~----~

Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

-~----------~----~----~----~------~----~------~--~---

[taua...@gmail.com]

Dear Guangchuang,

How can you use font face in italic and bold at the same time?

Thanks!

On Monday, June 19, 2017 at 12:15:39 AM UTC-4, Yu, Guangchuang wrote:

​

On Fri, Jun 16, 2017 at 6:01 PM, Frederik Bak <fba...@gmail.com> wrote:

Hi, 

I am trying to plot a tree where some of the tip labels are supposed to be bold and some are to be italic. 

I have read this: https://guangchuangyu.github.io/ggtree/faq/#formatting-tip-labels but it is still a bit unclear to me. 

I have thought about two ways to do it. One is: 

ggtree(phyloseqobject)+  geom_tiplab(aes(label=Name), align = TRUE, linetype = 0, offset = 0.04) + geom_text2(aes(label = label, fontface = "italic", subset=node %in% Mylist))+geom_text2(aes(label=label, fontface = "bold", subset = node %in% Mylist2))

Obviously, this plots the label names twice. I could off course skip the geom_tiplab part, but I really like the alignment which is made here. 

Another way could be something like:

I have not included the bold part in this one, but I assume it would just be adding another "+geom_tiplab(xxx)" afterwards?

ggtree(phyloseqobject) +  geom_tiplab(aes(subset = node %in% Mylist),label=substitute(italic(x),list(x=c(1:20)[1])), parse=T, align = TRUE, linetype = 0, offset = 0.04)

Here I get this error:

Warning: Ignoring unknown parameters: label, parse

Error: Aesthetics must be either length 1 or the same as the data (20): label, hjust

Mylist has the length 20 which is why I wrote c(1:20) (could has well been a vector with 20 labels). I do not know why this error occurs.

I think the latter option is the preferable one, in order to keep the alignment, but I need to be able to overcome the error.

Frederik

--
G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
 
Homepage: https://guangchuangyu.github.io/ggtree
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[Yu, Guangchuang]

pls try fontface='bold.italic'.

Homepage: https://guangchuangyu.github.io/software/ggtree

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--

--~--~---------~--~----~------------~-------~--~----~

Guangchuang Yu PhD

Professor
School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://guangchuangyu.github.io

-~----------~----~----~----~------~----~------~--~---

[Tauana Junqueira da Cunha]

Perfect, thanks!