Add ability to set `datanames` #824

llrs-roche · 2025-01-08T14:14:21Z

Pull Request

Fixes #821

This PR add a parameter (or uses existing ones) to use on teal::module(datanames) to select which datasets are shown in each module.

tm_file_viewer() doesn't have and I think shouldn't have.

Acceptance criteria:

tm_missing_data example

# general example data

library("devtools")
load_all("../teal.modules.general")
load_all("../teal.code")
load_all("../teal.transform")
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  
  add_nas <- function(x) {
    x[sample(seq_along(x), floor(length(x) * runif(1, .05, .17)))] <- NA
    x
  }
  
  iris <- iris
  .iris <- iris
  iris2 <- iris
  mtcars <- mtcars
  
  iris[] <- lapply(iris, add_nas)
  .iris[] <- lapply(.iris, add_nas)
  iris2[] <- lapply(iris2, add_nas)
  mtcars[] <- lapply(mtcars, add_nas)
  mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
  mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
})

app <- init(
  data = data,
  modules = modules(
    tm_missing_data(datasets_selected = c("iris2", "iris"))
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

tm_variable_browser example

library("devtools")
load_all("../teal.modules.general")
load_all("../teal.code")
load_all("../teal.transform")
# general data example
data <- teal_data()
data <- within(data, {
  iris <- iris
  mtcars <- mtcars
  women <- women
  faithful <- faithful
  CO2 <- CO2
})

app <- init(
  data = data,
  modules = modules(
    tm_variable_browser(
      label = "Variable browser",
      datasets_selected = c("iris", "mtcars")
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

tm_front_page (additional modifications to enable granular selection): Example

library("devtools")
load_all("../teal.modules.general")
load_all("../teal.code")
load_all("../teal.transform")
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- teal.data::rADSL
  ADSL2 <- ADSL
  attr(ADSL, "metadata") <- list("Author" = "NEST team", "data_source" = "synthetic data")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

table_1 <- data.frame(Info = c("A", "B"), Text = c("A", "B"))
table_2 <- data.frame(`Column 1` = c("C", "D"), `Column 2` = c(5.5, 6.6), `Column 3` = c("A", "B"))
table_3 <- data.frame(Info = c("E", "F"), Text = c("G", "H"))

table_input <- list(
  "Table 1" = table_1,
  "Table 2" = table_2,
  "Table 3" = table_3
)

app <- init(
  data = data,
  modules = modules(
    tm_front_page(
      header_text = c(
        "Important information" = "It can go here.",
        "Other information" = "Can go here."
      ),
      tables = table_input,
      additional_tags = HTML("Additional HTML or shiny tags go here <br>"),
      footnotes = c("X" = "is the first footnote", "Y is the second footnote"),
      show_metadata = TRUE,
      datasets_selected = "ADSL2"
    )
  ),
  header = tags$h1("Sample Application"),
  footer = tags$p("Application footer"),
)

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

I checked via searching datanames = that there are now at least 15 cases in module() corresponding to the 15 modules exported.

There is one that is not configurable (datanames = NULL on the picture above), tm_file_viewer. In my opinion it doesn't matter the datasets available on the module to visualize files. But if needed we can add a dataset_selected argument.

Note that I added the dataset_selected argument to two modules on the best place I thought, if a package/user is using positional arguments it might break (and also teal.gallery).

Note that it doesn't show on shinylive (on Rstudio, preview, not sure if once fully installed) and also that it doesn't show the url (this could be an issue with my machine):

github-actions · 2025-01-08T14:44:59Z

Unit Tests Summary

1 files 22 suites 13m 8s ⏱️
145 tests 107 ✅ 38 💤 0 ❌
476 runs 438 ✅ 38 💤 0 ❌

Results for commit f23555d.

♻️ This comment has been updated with latest results.

github-actions · 2025-01-08T14:45:03Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_pca	💔	$115.73$	$+2.77$	$0$	$0$	$0$	$0$
shinytest2-tm_front_page	💔	$20.34$	$+1.01$	$0$	$0$	$0$	$0$
shinytest2-tm_g_association	💔	$30.17$	$+1.60$	$0$	$0$	$0$	$0$
shinytest2-tm_g_bivariate	💔	$73.71$	$+1.29$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplot	💔	$72.89$	$+1.11$	$0$	$0$	$0$	$0$
shinytest2-tm_t_crosstable	💔	$31.18$	$+1.16$	$0$	$0$	$0$	$0$

Results for commit 101cc5c

♻️ This comment has been updated with latest results.

gogonzo · 2025-01-09T09:30:42Z

R/tm_front_page.R

+  datanames <- if (show_metadata && length(datasets_selected) > 0L) {
+    datasets_selected
+  } else if (show_metadata) {
+    "all"
+  } else {
+    NULL
+  }


There is a gap here when show_metadata = FALSE and length(datasets_selected). This show_metadata argument is unnecessary and I would suggest to deprecate show_metadata and to show metadata when datasets_selected is not empty. So:

tm_front_page <- function( datasets_selected = NULL, show_metadata = <deprecated> )

On that condition show_metadata prevails and nothing would be shown... but I can deprecate show_metadata entirely.

gogonzo · 2025-01-09T09:34:49Z

R/tm_missing_data.R

@@ -110,6 +111,7 @@
 tm_missing_data <- function(label = "Missing data",
                            plot_height = c(600, 400, 5000),
                            plot_width = NULL,
+                            datasets_selected = character(0L),


if this argument was named datanames it would be inherited from teal::module.

I went with what is used in other modules, currently there are 2 modules using this argument: tm_data_table and tm_variable_browser. Let me know if you want me to rename those other modules too.
I haven't tested what happens with transformators...

I think it would be much easier if tm_data_table and tm_variable_browser had datanames instead of datasets_selected . I wouldn't rename them, but:

datanames = "all", datasets_selected = <deprecated>

I will do that and check what happens with transformators.

llrs-roche added 5 commits January 8, 2025 13:14

Add datasets_selected argument

9d52672

Use datasets_selected for datanames

4cab9d5

Add datasets_selected

01af1e5

Improve checks on datasets_selected

7d1d1e9

Rstudio new version adds an id

f64f3a0

llrs-roche added the core label Jan 8, 2025

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

f23555d

gogonzo reviewed Jan 9, 2025

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add ability to set `datanames` #824

Add ability to set `datanames` #824

llrs-roche commented Jan 8, 2025 •

edited

Loading

github-actions bot commented Jan 8, 2025 •

edited

Loading

github-actions bot commented Jan 8, 2025 •

edited

Loading

gogonzo Jan 9, 2025

llrs-roche Jan 9, 2025

gogonzo Jan 9, 2025

llrs-roche Jan 9, 2025

gogonzo Jan 9, 2025

llrs-roche Jan 9, 2025

Add ability to set datanames #824

Are you sure you want to change the base?

Add ability to set datanames #824

Conversation

llrs-roche commented Jan 8, 2025 • edited Loading

Pull Request

github-actions bot commented Jan 8, 2025 • edited Loading

Unit Tests Summary

github-actions bot commented Jan 8, 2025 • edited Loading

Unit Test Performance Difference

gogonzo Jan 9, 2025

Choose a reason for hiding this comment

llrs-roche Jan 9, 2025

Choose a reason for hiding this comment

gogonzo Jan 9, 2025

Choose a reason for hiding this comment

llrs-roche Jan 9, 2025

Choose a reason for hiding this comment

gogonzo Jan 9, 2025

Choose a reason for hiding this comment

llrs-roche Jan 9, 2025

Choose a reason for hiding this comment

Add ability to set `datanames` #824

Add ability to set `datanames` #824

llrs-roche commented Jan 8, 2025 •

edited

Loading

github-actions bot commented Jan 8, 2025 •

edited

Loading

github-actions bot commented Jan 8, 2025 •

edited

Loading