flextable

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Hi! First off, thanks for this great package, I'm always amazed at all it can achieve.

I've come across what I think is a bug, but it may be a deliberate feature since the update that you mention in #395. I had created a table containing p-values, where the background of the cells was coloured using scales::col_numeric() as suggested, but only if they fell within a certain range (p < 0.05).

colourer <- scales::col_numeric(
    palette = c("darkgreen", "green"),
  domain = c(0, 0.05), na.color = "#FFFFFF"
)

my_data <- tibble(p1 = c(0.5, 0.01, 0.1, 0.002),
                  p2 = c(0.5, 0.02, 0.1, 0.001))

my_data %>%
  flextable::flextable() %>%
  flextable::bg(part = "body", bg = colourer)

Since updating the package, I get the following error:

Error: a warning occured while using color function: Some values were outside the color scale and will be treated as NA

I realise this may be deliberate, but restricting the domain to those values (p between 0 and 0.05) makes good use of the colour palette within the range we're interested in, while allowing us to ignore other values. Would it be possible to throw a warning that still allows the table to be created?

Thanks!

I've found a work-around of turning the values we're not interested in into NAs before piping into flextable in the meantime. Happy to stick with this if that's the best plan.

my_data <- tibble(comparison = c("A", "B", "C", "D"),
                  p1 = c(0.5, 0.01, 0.1, 0.002),
                  p2 = c(0.5, 0.02, 0.1, 0.001))

my_data %>%
  mutate_at(-1, function(x) ifelse(x < 0.05, x, NA)) %>%
  flextable::flextable() %>%
  flextable::bg(j = 2:3, part = "body", bg = colourer)

Hello,

Could you post your sessionInfo() please as asked in the guidelines? I am confused because I can't reproduce your issue.

I have a warning (from scales::col_numeric()) but no error.

library(flextable)
library(magrittr)
library(tibble)

colourer <- scales::col_numeric(
  palette = c("darkgreen", "green"),
  domain = c(0, 0.05), na.color = "red"
)

my_data <- tibble(p1 = c(0.5, 0.01, 0.1, 0.002),
                  p2 = c(0.5, 0.02, 0.1, 0.001))

my_data %>%
  flextable() %>%
  bg(part = "body", bg = colourer)
#> Warning: Some values were outside the color scale and will be treated as NA

#> Warning: Some values were outside the color scale and will be treated as NA

^{Created on 2022-08-07 by the reprex package (v2.0.1)}

Sorry for the delay in getting back to you, and for the omission.

Here's the session info. I just reproduced the error using the code snippet you provided in a new R session.

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] tibble_3.1.7    magrittr_2.0.3  flextable_0.7.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7        rstudioapi_0.13   knitr_1.39        xml2_1.3.3       
 [5] munsell_0.5.0     uuid_1.0-3        colorspace_2.0-3  R6_2.5.1         
 [9] rlang_1.0.2       fastmap_1.1.0     fansi_1.0.3       tools_4.1.2      
[13] data.table_1.14.2 xfun_0.31         utf8_1.2.2        cli_3.3.0        
[17] htmltools_0.5.2   systemfonts_1.0.3 ellipsis_0.3.2    digest_0.6.29    
[21] lifecycle_1.0.1   crayon_1.5.1      zip_2.2.0         farver_2.1.0     
[25] officer_0.4.1     vctrs_0.4.1       base64enc_0.1-3   glue_1.6.2       
[29] evaluate_0.15     rmarkdown_2.14    compiler_4.1.2    pillar_1.7.0     
[33] scales_1.2.0      gdtools_0.2.3     pkgconfig_2.0.3  

The error message was:

Error: a warning occured while using color function: Some values were outside the color scale and will be treated as NA

No problem for the delay:)

Thanks, this has been fixed in version 0.7.3. Sorry for the inconvenience. Now, you would get a warning as in my previous reprex instead of an error. This warning just display the warning coming from package 'scales'.

I do not recommend using your workaround because it changes the data (although you get your work done!). I would instead either accept the warning from 'scales', either write a wrapper around it as shown below; that way, we don't need to change the data.

library(dplyr)
colourer <- function(x, myrange = c(0, 0.05)){
  scale_colourer <- scales::col_numeric(
    palette = c("darkgreen", "green"),
    domain = myrange, na.color = "#FFFFFF"
  )
  colors <- rep("transparent", length(x))
  withinrange <-between(x, left = myrange[1], right = myrange[2])
  colors[withinrange] <- scale_colourer(x[withinrange])
  colors
}
my_data <- tibble(p1 = c(0.5, 0.01, 0.1, 0.002),
                  p2 = c(0.5, 0.02, 0.1, 0.001))

my_data %>%
  flextable::flextable() %>%
  flextable::bg(part = "body", bg = colourer)

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