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feature request: allowing parsing #64

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IndrajeetPatil opened this issue Jul 2, 2019 · 5 comments
Closed

feature request: allowing parsing #64

IndrajeetPatil opened this issue Jul 2, 2019 · 5 comments

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@IndrajeetPatil
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ggplot and some of its extensions (e.g, ggrepel) allow the labels to be parsed into expressions and displayed as described in plotmath. But, as far as I understand ggsignif, this is currently possible?

Will you consider supporting it? Thanks.

# setup
library(tidyverse)
library(ggsignif)

# creating a dataframe 
(df <- tibble::tribble(
  ~x, ~lab,
  1, "p < 0.001",
  2, paste("list(~italic(p)<=", "0.001", ")", sep = "")
))
#> # A tibble: 2 x 2
#>       x lab                    
#>   <dbl> <chr>                  
#> 1     1 p < 0.001              
#> 2     2 list(~italic(p)<=0.001)

# ggplot supports parsing
ggplot(mtcars, aes(am, wt)) + geom_point() + 
  labs(x = parse(text = df$lab[2]))

# ggsignif doesn't
ggplot(mpg, aes(class, hwy)) +
  geom_boxplot() +
  geom_signif(comparisons = list(c("compact", "pickup")), 
              annotations = parse(text = df$lab[2]))
#> Warning: Computation failed in `stat_signif()`:
#> cannot coerce class '"expression"' to a data.frame

Created on 2019-07-02 by the reprex package (v0.3.0)

Session info 
devtools::session_info()
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@const-ae
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const-ae commented Jul 2, 2019

Hi Indrajeet,
thank you for the suggestion, this would definitely be a useful addition. I will try and see how difficult it is to add it, when I find some time. However, if anyone (or you) would be interested in giving it a try, I would also be very happy to accept a pull request.
Best, Constantin

@cloudbroken
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cloudbroken commented Aug 4, 2019 •
edited
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Agree this would be a useful feature.
In the meantime this is a hacked together function which produces scientific notation for p values with ggsignif.

  library(ggplot2)
  library(ggsignif)
  
  # function to format a numeric p-value in scientific notation
  # max_pd parameter refers to max decimal places before switching to scientific notation. Otherwise the full decimal is displayed.
  # p-values are given to one significant digit
  
  pform <- function(p, max_dp = 4) {
    # map the superscript versions of numbers (obtained from https://en.wikipedia.org/wiki/Unicode_subscripts_and_superscripts)
    ucmap <- c("0" = "\u2070",
               "1" = "\u00B9",
               "2" = "\u00B2",
               "3" = "\u00B3",
               "4" = "\u2074",
               "5" = "\u2075",
               "6" = "\u2076",
               "7" = "\u2077",
               "8" = "\u2078",
               "9" = "\u2079",
               "-" = "\u207B")
    
    pe <- formatC(signif(p,1), digits = 0, format = "e")
    
    pv <- unlist(strsplit(pe, split = "e"))
    
    if(abs(as.numeric(pv[2])) > max_dp) {
      
      pv2 <- as.character(as.numeric(pv[2]))
      
      pv2v <- unlist(strsplit(pv2, split = ""))
      
      ps <- paste(ucmap[pv2v], sep = "", collapse = "")
      
      paste(pv[1],"x10", ps, collapse = "", sep = "")
      
      
    } else {
      formatC(signif(p,1), digits = max_dp, format = "f", drop0trailing = T)
    }
  }
  
  
  # test
  ggplot(mpg, aes(class, hwy)) +
    geom_boxplot() +
    geom_signif(comparisons = list(c("compact", "pickup")), 
                map_signif_level = pform)

image

Otherwise thank you for a supremely useful package!

const-ae added a commit that referenced this issue Aug 5, 2019
@const-ae
Fix issue #64: Enable plotmath
c4d79df
@const-ae
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const-ae commented Aug 5, 2019

Hi,
I finally got around to implemented the parsing of plotmath expressions.

Note that you have to call the function with annotations set to a string that is internally parsed, if parse=TRUE. This follows the example of geom_text() and is different from labs().

# setup
library(tidyverse)
library(ggsignif)

# creating a dataframe 
(df <- tibble::tribble(
  ~x, ~lab,
  1, "p < 0.001",
  2, paste("list(~italic(p)<=", "0.001", ")", sep = "")
))
#> # A tibble: 2 x 2
#>       x lab                    
#>   <dbl> <chr>                  
#> 1     1 p < 0.001              
#> 2     2 list(~italic(p)<=0.001)

# ggplot supports parsing
ggplot(mtcars, aes(as.character(am), wt)) + 
  geom_point() + 
  geom_signif(annotations = df$lab[2], comparisons = list(c("0", "1"))) +
  labs(x = parse(text = df$lab[2]))

# ggplot supports parsing
ggplot(mtcars, aes(as.character(am), wt)) + 
  geom_point() + 
  geom_signif(annotations = df$lab[2], comparisons = list(c("0", "1")),
              parse=TRUE) +
  labs(x = parse(text = df$lab[2]))

Created on 2019-08-05 by the reprex package (v0.3.0)

It would be great if you could test if this solves your issue. If so, I would try to push an updated version to CRAN in the coming days.

Best, Constantin

@IndrajeetPatil
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Dear Constantin,

Thank you so much for implementing this! I can confirm that this is working as expected.

@const-ae
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const-ae commented Aug 8, 2019

The update version is now on CRAN :)

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@const-ae @cloudbroken @IndrajeetPatil