CODEWITHSUNDEEP
rgtsummary
Pascal Schmidt
Pascal Schmidt

Reputation: 243

Set values default theme and bold variables for gtsummary package

I have a question regarding setting the default theme for the gtsummary package.

library(tidyverse)
library(gtsummary)
library(gapminder)

gap <- gapminder %>% 
  dplyr::mutate_all(~ifelse(
    sample(c(TRUE, FALSE), size = length(.), replace = TRUE, prob = c(0.8, 0.2)),
    as.character(.), 
    NA)
  ) %>% 
  dplyr::mutate_at(vars(year:gdpPercap), ~as.numeric(.)
  ) %>% 
  dplyr::mutate(gdpPercap = ifelse(gdpPercap > median(gdpPercap, na.rm = TRUE), "high", "low"))

my_theme <-   
  list(
    "tbl_summary-str:default_con_type" = "continuous2",
    "tbl_summary-str:continuous_stat" = c("{median} ({p25} - {p75})",
                                          "{mean} ({sd})", 
                                          "{min} - {max}"),
    "tbl_summary-str:categorical_stat" = "{n} / {N} ({p}%)",
    "style_number-arg:big.mark" = "",
    "add_p.tbl_summary-attr:test.categorical" = "",
    "tbl_summary-fn:percent_fun" = function(x) style_percent(x, digits = 3),
    "add_p.tbl_summary-attr:test.categorical" = "chisq.test"
  )

gap %>% 
  gtsummary::tbl_summary(
    by = continent
  )

I would like to know how I can set the default theme to add p values or for example make the labels bold. I tried the code above but it did not work. I know that I can add add_p() but I would like to know if I can do that in the theme so I don't have to type add_p when wanting to add p-values. Thank you for your help.

Upvotes: 2

Views: 1130

Answers (1)

Daniel D. Sjoberg
Daniel D. Sjoberg

Reputation: 11754

UPDATE: As of gtsummary v1.4.0, you can set functions like add_p() and bold_labels() after each tbl_summary() using themes.

library(gtsummary)
packageVersion("gtsummary")
#> [1] '1.4.0'

# theme to always run add_p() and bold_labels() after tbl_summary()
list(
  "tbl_summary-fn:addnl-fn-to-run" = 
    function(x) {
      if (!is.null(x$by)) x <- add_p(x) # add_p if there is a by variable
      bold_labels(x) # bold labels and return table
    }
  ) %>%
  set_gtsummary_theme()

tbl <-
  trial %>%
  select(age, grade, trt) %>%
  tbl_summary(by = trt)

enter image description here Created on 2021-04-14 by the reprex package (v2.0.0)

OLD POST: There is no way to directly run add_p() and bold_labels() automatically after tbl_summary() using themes. I think the your best bet may be to define a new function that runs the additional functions.

tbl_summary_p <- function(...) {
  tbl_summary(...) %>%
    add_p() %>%
    bold_labels()
}

gap %>% tbl_summary_p(by = continent)

You can, however, utilize the themes to bold the labels. Themes allow you to include any formatting commands using theme element as_gt-lst:addl_cmds. If you add the theme element below to your theme list, gt tables will have the label rows bolded.

# bold labels for gt output
  "as_gt-lst:addl_cmds" = 
    list(tab_spanner = expr(gt::tab_style(style = gt::cell_text(weight = "bold"), 
                                          locations = gt::cells_body(columns = gt::vars(label), 
                                                                     rows = row_type == "label"))))

Upvotes: 2

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