Error in parse(text ...) unexpected comma "," when plotting ggplot with ggpubr::stat

Having set the output decimal to a comma with the option command I get the following error, when using the function stat_cor to include Pearson correlation results in a ggplot:

Error in parse(text = text[[i]]) : <text>:1:16: unexpected ','
1: italic(R)~`=`~0,
                  ^

Below a minimal reproducible example:

library(ggplot2)
library(ggpubr)

options(OutDec= ",") #set decimal seperator to a comma
 
plot<-ggplot(economics,aes (x=pce/10000, y=uempmed))   
  geom_point(size = 2) 
plot #works fine and axis labels correctly have commas as decimal seperator

options(OutDec= ",") #set decimal seperator to a comma

plot<-ggplot(economics,aes (x=pce/10000, y=uempmed))   
  geom_point(size = 2) 
  stat_cor(show.legend = F ,label.y = c(18), method = "pearson") 
plot #ERROR, adding ,decimal.mark = "," does not work

#Leads to error:
#Error in parse(text = text[[i]]) : <text>:1:16: unexpected ','
#1: italic(R)~`=`~0,
#                   ^

options(OutDec= ".") #set decimal seperator to a dot and it works as expected

plot<-ggplot(economics,aes (x=pce/10000, y=uempmed))   
  geom_point(size = 2) 
  stat_cor(show.legend = F ,label.y = c(18), method = "pearson")
plot #correct output

I searched through the help functions to see which arguments can be passed to stat_cor and it leads to other arguments to pass to geom_text or geom_label. and there to Other arguments passed on to layer(). So I tried including ,decimal.mark = "," and , labels = label_number(decimal.mark = "," ) in the stat_cor function but that did not work.

This is the closest thing I have found while googling but it did not help me as it is the same problem but in a different function (geom_sf) https://github.com/tidyverse/ggplot2/issues/3365 However, I think there the root of the issue is explained:

**clauswilke commented on Jun 17, 2019 ** As far as I can tell, this particular problem arises because ggplot creates a plotmath expression, then converts it into a string, and then parses the string again. At that parsing stage, the number with a comma as separator is not understood.

I guess there could be a workaround by using geom_annotate or geom_label but that means I would have to manually include all of the pearson correlation test results for a lot of graphs so I would prefer a direct fix.

CodePudding user response：

This is a bug in the package ggpubr as it cannot handle commas as decimal seperators. For more information see here or in the comments:

MrFlick: Specifically I think it's in this line https://github.com/kassambara/ggpubr/blob/ac5a01f586a5f0b47260fed071e79be36ef3f8ea/R/stat_cor.R#L207 . Those values should be wrapped in quotes to prevent the parsing error. And the problem with the persistent decimal point in the p-values comes from https://github.com/kassambara/ggpubr/blob/ac5a01f586a5f0b47260fed071e79be36ef3f8ea/R/stat_cor.R#L219 . It doesn't look like the package really support a comma separator. –

However, there is a workaround (pointed out by @MrFlick) by passing the argument , output.type="text" in the stat_cor function e.g.:

stat_cor(show.legend = F ,label.y = c(18), method = "pearson", output.type="text")

However, there is an edge case where this does not work, if p < 2.2e-16 (as with the example data) as the value of p is passed as a string and not a number. Otherwise it works though.