plot_beeswarm retired functions

[fontikar]

---

author: fontikar
date: 2021-06-15
output: "reprex::reprex_document"
title: steep-carp_reprex.R

Can't convert old retired functions into their new recommended ones. Suspect it is actually a bug in scales! I have lodged an issue with them - scary stuff. This isn't super high priority because even retired functions takes a while to become completely obsolete and unusable (Wickham, useR 2021).

library(scales)
library(patchwork)

# Old retired code that needs to be updated following scales recommendations
#"parse_format() and math_format() was retired; please use label_parse() and label_math() instead"
demo_log10(x = c(0.1, 10e07),
           breaks = scales::trans_breaks("log10", function(x) 10^x),
           labels = scales::trans_format("log10", scales::math_format(10^.x)))
#> scale_x_log10(breaks = scales::trans_breaks("log10", function(x) 10^x), 
#>     labels = scales::trans_format("log10", scales::math_format(10^.x)))

#Lets do the breaks first
demo_log10(x = c(0.1, 10e07),
           breaks = trans_breaks("log10", function(x) 10^x)) #Old retired code
#> scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x))

demo_log10(x = c(0.1, 10e07),
           breaks = breaks_log(6)) #YAY easy conversion
#> scale_x_log10(breaks = breaks_log(6))

#Now the labels
demo_log10(x = c(0.1, 10e07),
           breaks = breaks_log(6), 
           labels = trans_format("log10", scales::math_format(10^.x))) #Old retired code
#> scale_x_log10(breaks = breaks_log(6), labels = trans_format("log10", 
#>     scales::math_format(10^.x)))

lab_math <- demo_log10(x = c(0.1, 10e07),
           breaks = breaks_log(6), 
           labels = scales::label_math()) #The superscript is not what is expected
#> scale_x_log10(breaks = breaks_log(6), labels = scales::label_math())

lab_number <- demo_log10(x = c(0.1, 10e07),
                       breaks = breaks_log(6), 
                       labels = scales::label_number()) #Original labels
#> scale_x_log10(breaks = breaks_log(6), labels = scales::label_number())

lab_math/lab_number

^{Created on 2021-06-15 by the reprex package (v2.0.0)}

[fontikar]

Using a bbolker function for now! Suggested here: r-lib/scales#311
format = log10 gives weird labels still especially if range is not very big, hard to generalise function that will also accomodate varying breaks, so this is a good solution for now! Also deals with issue #12 so I will close both!

p1 <- p1 + scale_x_log10(name="", breaks = scales::breaks_log(), labels = scientific_10, limits=c(vals$minimum, vals$maximum)) p2 <- p2 + scale_x_log10(name=paste(plant_trait_name, ' (', data$unit[1], ')'), breaks = scales::breaks_log(), labels = scientific_10, limits=c(vals$minimum, vals$maximum))