gtsummary support in table_with_settings

[m7pr]

Fix

• [Feature Request]: Upgrade table_with_settings to accept gtsummary object #335

Idea, we extract export_table and render_table_to_html out of the existing functionality for rtables and we add a dispatch for gt_tbl and gtsummary objects :)

Tested with

library(shiny)
library(rtables)
library(gtsummary)
library(gt)
library(magrittr)

ui <- bslib::page_fluid(
  table_with_settings_ui(id = "rtables_table"),
  table_with_settings_ui(id = "gtsummary_table"),
  table_with_settings_ui(id = "gt_table")
)

server <- function(input, output, session) {
  table_r_rtables <- reactive({
    l <- basic_table() %>%
      split_cols_by("ARM") %>%
      analyze(c("SEX", "AGE"))
    build_table(l, DM)
  })

  table_r_gtsummary <- reactive({
    gtsummary::tbl_summary(mtcars)
  })

  table_r_gt <- reactive({
    mtcars %>%
      gt::gt() %>%
      gt::tab_header(title = "Motor Trend Car Road Tests")
  })

  table_with_settings_srv(id = "rtables_table", table_r = table_r_rtables)
  table_with_settings_srv(id = "gtsummary_table", table_r = table_r_gtsummary)
  table_with_settings_srv(id = "gt_table", table_r = table_r_gt)
}

if (interactive()) {
  shinyApp(ui, server)
}

gtsummary

PDF export

CSV export

TEXT export

gt

PDF export

CSV export

TEXT export

[m7pr]

Hey @llrs-roche and @gogonzo
Before going further, just wanted to consult the idea of implementing support for gt and gtsummary inside table_with_settings.

I though we can dispatch the current approach implement for rtables, to support gt and gtsummary objects. For now there are placeholder. What do you think? If you give it a green light, I'll try to fill placeholders with actual implementation

[llrs-roche]

I think using dispatch is the best approach. This way we can support new objects like on #334
The class, file, format abstraction should work well in my opinion 👍

[gogonzo]

Looks very good ⭐

[github-actions]

Code Coverage Summary

Filename                      Stmts    Miss  Cover    Missing
--------------------------  -------  ------  -------  ------------------------------------------------------
R/basic_table_args.R             23       0  100.00%
R/draggable_buckets.R            87      12  86.21%   116-121, 151-156
R/get_dt_rows.R                  13       0  100.00%
R/ggplot2_args.R                 49       0  100.00%
R/nested_closeable_modal.R       20      20  0.00%    83-103
R/optionalInput.R               255      79  69.02%   190, 315-389, 402-409, 411-416, 434, 436, 501, 583-596
R/panel_group.R                  39      39  0.00%    50-136
R/plot_with_settings.R          309      16  94.82%   299-305, 327, 364, 373-374, 390, 578-579, 581, 583
R/standard_layout.R              52       4  92.31%   90-93
R/table_with_settings.R         199      24  87.94%   32-36, 82, 127-158
R/utils.R                         7       0  100.00%
R/verbatim_popup.R              105      35  66.67%   113-114, 116, 124-155
R/white_small_well.R              7       0  100.00%
TOTAL                          1165     229  80.34%

Diff against main

Filename                   Stmts    Miss  Cover
-----------------------  -------  ------  -------
R/table_with_settings.R      +41     +23  -11.43%
TOTAL                        +41     +23  -1.33%

Results for commit: c011502

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   16 suites   1m 51s ⏱️
172 tests 172 ✅ 0 💤 0 ❌
399 runs  399 ✅ 0 💤 0 ❌

Results for commit c011502.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
plot_with_settings_ui	💚	$52.45$	$-3.04$	$0$	$0$	$0$	$0$
table_with_settings	💔	$2.20$	$+1.20$	$+7$	$0$	$0$	$0$
table_with_settings_ui	💚	$33.12$	$-1.27$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
table_with_settings	👶		$+0.19$	table_with_settings_srv_gt_table_renders_with_content
table_with_settings	👶		$+1.26$	table_with_settings_srv_gtsummary_table_renders_with_content
table_with_settings	💀	$0.12$	$-0.12$	table_with_settings_srv_return_html_table
table_with_settings	👶		$+0.10$	table_with_settings_srv_return_html_table_with_content

Results for commit c0c18fc

♻️ This comment has been updated with latest results.

[m7pr]

Amazing, I will proceed with implementation, some examples and finally with tests

[llrs-roche]

Looks almost ready.

For the text format of gtsummary could we use like a table with write.table() but without quotes? It will be easier to read than the html as it includes many tags, attrigutes and some elements that are out of the table:

<div id="uftobyoadg" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">

But I'm not really sure who will use the text format of gtsummary. If this is for reporting it won't look good.

Not sure what I missed but the tests don't seem to cover anything from the file (but at the same time the CI only reports a 1% decrease)

covr::file_coverage("R/table_with_settings.R", "tests/testthat/test-table_with_settings.R")
Test passed with 2 successes 🥳.
Test passed with 1 success 🥇.
Test passed with 3 successes 😸.
Test passed with 1 success 😸.
Test passed with 6 successes 😀.
Test passed with 6 successes 🎉.
Test passed with 6 successes 🥳.
Test passed with 2 successes 🌈.
Test passed with 1 success 🌈.
Test passed with 1 success 🎊.
Test passed with 3 successes 🥳.
Test passed with 3 successes 🥳.
Coverage: 0.00%
R/table_with_settings.R: 0.00%

[m7pr]

Hey @llrs-roche I applied your feedback.

• TEXT export looks better now (I updated print-screens in the initial PR descripion).
• The example was also updated, and now it shows the difference of 3 different supported objects in one shiny app.
• Also adjusted and simplified implementation

If you accept I will try to remove formatters and rtables from Remotes, before I merge

[llrs-roche]

gt text export should not print the X1, X2, X3 if possible other than that I am a bit unsure about all the methods and how they are used. But let's merge it.

Remember to test without the dev versions of rtables and formatters and to fix the style and lintr checks.

One last question. Is it possible to test the file downloaded/generated? I'm just wondering if we can test that it produces something without writing to the temp folder

[m7pr]

@llrs-roche I was able to cleanup gt objects, so the title of the table is dropped and we only save the data in text output

[m7pr]

Remember to test without the dev versions of rtables and formatters and to fix the style and lintr checks.

Will test now!

One last question. Is it possible to test the file downloaded/generated? I'm just wondering if we can test that it produces something without writing to the temp folder

No idea. I think we should be able to test the content of the file that is saved to temp folder.
Without writing we are testing the content of the object in table_with_settings_srv testServer tests.

We've got this

testthat::test_that("table_with_settings_srv: gt table renders with content", {
  gt_r <- shiny::reactive({
    gt::gt(mtcars[1:5, 1:3])
  })

  shiny::testServer(
    teal.widgets::table_with_settings_srv,
    args = list(id = "tws", table_r = gt_r),
    expr = {
      html_content <- as.character(output$table_out_main$html)
      testthat::expect_s3_class(output$table_out_main$html, "html")
      testthat::expect_true(grepl("mpg|cyl|disp", html_content, ignore.case = TRUE))
      testthat::expect_true(grepl("<table", html_content, ignore.case = TRUE))
    }
  )
})