Question

Math expression in shapeCustom legend in EnhancedVolcano

0

Entering edit mode

pl23 • 0

@4b83ad99

Last seen 8 days ago

Canada

Hello,

I want to incorporate mathematical expressions in my legend for shapeCustom but am not sure of how to do so. When setting up my keyvals.shape vector, I tried using names with R expression() but this doesn't seem to work. Does anyone have any suggestions? In particular, suppose I have two shapes, one where I want the legend to be log_10(p)>50 and one with log_10(p)<=50 (expressed with subscripts and math symbols). How do I go about doing this?

Thank you!

EnhancedVolcano • 315 views

ADD COMMENT • link 9 days ago • updated 8 days ago pl23 • 0

score 1 · Accepted Answer · 2024-04-25

1

Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

Use bquote. See section 4.6 in the vignette.

ADD COMMENT • link 9 days ago James W. MacDonald 65k

0

Entering edit mode

Hi,

Yes, I've tried this, but I am not sure if it is possible to assign bquote values to the names of a vector. In particular, if I use an ifelse statement, I get

> keyvals.shape = c(rep(3,10), rep(2,8))
> names(keyvals.shape) = ifelse(keyvals.shape==3, bquote(-log[10]*p >= 50),bquote(-log[10]*p<50))
Error in rep(yes, length.out = len) : 
  attempt to replicate an object of type 'language'

On the other hand, if I try to set names as a character before assigning the values, I get the following error:

> names(keyvals.shape) = "a"
> names(keyvals.shape)[keyvals.shape==3] = bquote(-log[10]*p >= 50)
Error in names(keyvals.shape)[keyvals.shape == 3] = bquote(-log[10] *  : 
  incompatible types (from language to character) in subassignment type fix

I am not too familiar with these functionalities in R, so I'd appreciate any suggestions. Thank you!

ADD REPLY • link 9 days ago pl23 • 0

0

Entering edit mode

Ah, good point. You could instead try

> library(ggtext)
> keyvals.shape = c(rep(3,10), rep(2,8))
> names(keyvals.shape) = ifelse(keyvals.shape==3, "-log<sub>10</sub>*p≥50", "-log<sub>10</sub>*p>50")
## and then 
> EnhancedVolcano(<args go here>) + theme(legend.text = element_markdown())

ADD REPLY • link 9 days ago James W. MacDonald 65k

0

Entering edit mode

Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal, which is ≥, and in the next instance it's <

ADD REPLY • link 9 days ago James W. MacDonald 65k

0

Entering edit mode

Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;

ADD REPLY • link 9 days ago James W. MacDonald 65k

0

Entering edit mode

So basically you are using HTML markup to set your subscripts and whatnot, and then element_markdown does the rest.

ADD REPLY • link 9 days ago James W. MacDonald 65k

0

Entering edit mode

Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown interpretation so I had to change those to the HTML notation as well.

ADD REPLY • link 8 days ago pl23 • 0