Display output on tm_data_table, tm_variable_browser, tm_missing_data by llrs-roche · Pull Request #829 · insightsengineering/teal.modules.general

llrs-roche · 2025-01-22T13:02:20Z

Pull Request

This PR works on the edge cases of datanames = "all" and NULL for each three modules, in addition I also revised the decision on tm_front_page to show all modules by default, and reverted back to not showing the panels by default, as per previous behavior and @vedhav compelling comment.

Code used to check this (besides the examples)

library("teal")
devtools::load_all("../teal.modules.general")

data <- teal_data()
data <- within(data, {
  library(dplyr)
  IRIS <- iris
  MTCARS <- mtcars
  # ADSL <- teal.data::rADSL
})

datanames <- "all"

app <- init(
  data = data,
  modules = modules(
    example_module(),
    tm_front_page(datanames = datanames),
    tm_data_table(datanames = datanames),
    tm_variable_browser(datanames = datanames),
    tm_missing_data(datanames = datanames)
  )
)

shinyApp(app$ui, app$server)


datanames <- NULL

app <- init(
  data = data,
  modules = modules(
    example_module(),
    tm_front_page(datanames = datanames),
    tm_data_table(datanames = datanames),
    tm_variable_browser(datanames = datanames),
    tm_missing_data(datanames = datanames)
  )
)

shinyApp(app$ui, app$server)

module	"all"	NULL
`tm_data_table()`	✅	✅ 1
`tm_variable_browser()`	✅	✅ 2
`tm_missing_data()`	✅	✅ 2

1: No right-panel but the table uses all datasets that are data.frames. I was thinking if variables_selected names should be used when datanames is NULL ? So that something like this should only show IRIS dataset and no left panel.

teal.modules.general::tm_data_table(
   datanames = NULL,
   variables_selected = list(IRIS = colnames(data$IRIS)[1:3])),

But this gets complicated if one wants to keep the standard 6 columns of the datasests as assertion fails:

teal.modules.general::tm_data_table(
  datanames = NULL,
  variables_selected = list(IRIS = colnames(data$IRIS)[1:3], MTCARS = NULL)),

Assertion on 'variables_selected' failed: May only contain the following types: {character}, but element 2 has type 'NULL'.

2: No right-panel but all the datasets that are data.frames are shown.

I also tested whether transformators worked with tm_missing_data (the only one of these three modules with a transformator argument) because the datanames documentation implies it will be merged with it: currently it doesn't and I'm not sure how to fix it.

If I create a transformator and use datanames not equal to all by default the new dataname won't be used.
I need to explore better the interaction between teal::module and the transformator.

reprex with transformators

library("teal")

data <- teal_data()
data <- within(data, {
  library(dplyr)
  IRIS <- iris
  MTCARS <- mtcars
  # ADSL <- teal.data::rADSL
})


transf <- list(teal_transform_module(
  label = "Transformator",
  ui = function(id) {
    ns <- NS(id)
    tags$div(
      numericInput(ns("n_rows"), "Number of rows to subset", value = 32, min = 1, max = 150, step = 1)
    )
  },
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      reactive({
        within(data(),
               {
                 iris <- head(IRIS, num_rows)
               },
               num_rows = input$n_rows
        )
      })
    })
  },
  datanames = "all"
))


datanames <- "IRIS"

app <- init(
  data = data,
  modules = modules(
    example_module(),
    tm_front_page(datanames = datanames),
    tm_data_table(datanames = datanames),
    tm_variable_browser(datanames = datanames),
    tm_missing_data(datanames = datanames, transformators = transf)
  )
)

shinyApp(app$ui, app$server)

m7pr · 2025-01-22T13:13:04Z

@llrs-roche about transformators and datanames. Have you tried to unify names?
Looks like teal_data() only contains IRIS and MTCARS, however module uses only IRIS BUT your transformator tries to change iris

m7pr · 2025-01-24T09:09:00Z

@llrs-roche about this

teal.modules.general::tm_data_table(
  datanames = NULL,
  variables_selected = list(IRIS = colnames(data$IRIS)[1:3], MTCARS = NULL)),

Assertion on 'variables_selected' failed: May only contain the following types: {character}, but element 2 has type 'NULL'.

What you get if

teal.modules.general::tm_data_table(
  datanames = NULL,
  variables_selected = list(IRIS = colnames(data$IRIS)[1:3], MTCARS = character(0)),

m7pr · 2025-01-24T09:10:26Z

Or

MTCARS = names(mtcars)

llrs-roche · 2025-01-24T09:17:29Z

If I use

teal.modules.general::tm_data_table(
  datanames = NULL,
  variables_selected = list(IRIS = colnames(data$IRIS)[1:3], MTCARS = character(0)),

I get:

[INFO] 2025-01-24 10:13:21.1288 pid:10196 token:[] teal.modules.general Initializing tm_missing_data
[INFO] 2025-01-24 10:13:21.1341 pid:10196 token:[] teal.modules.general Initializing tm_data_table
[ERROR] 2025-01-24 10:13:21.1409 pid:10196 token:[] teal.modules.general In 'FUN(X[[i]], ...)': Assertion on 'variables_selected[[i]]' failed: Must have length >= 1, but has length 0.
Error in FUN(X[[i]], ...) : 
  Assertion on 'variables_selected[[i]]' failed: Must have length >= 1, but has length 0.
Calls: init ... lapply -> FUN -> <Anonymous> -> makeAssertion -> mstop

But passing MTCARS = colnames(mtcars) does show all the columns on the module

m7pr · 2025-01-24T09:20:29Z

When it comes to transformators, it shows the dataset if the new one has a different name than IRIS/iris

# general example data
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
  mtcars <- mtcars
  
  iris[] <- lapply(iris, add_nas)
  mtcars[] <- lapply(mtcars, add_nas)
  mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
  mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
})

transf <- teal_transform_module(
  label = "Transformator",
  ui = function(id) {
    ns <- NS(id)
    tags$div(
      numericInput(ns("n_rows"), "Number of rows to subset", value = 32, min = 1, max = 150, step = 1)
    )
  },
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      reactive({
        within(data(),
               {
                 im_new <- head(iris, num_rows)
               },
               num_rows = input$n_rows
        )
      })
    })
  }
)

app <- init(
  data = data,
  modules = modules(
    tm_missing_data(parent_dataname = "mtcars", transformators = list(transf))
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

llrs-roche · 2025-01-24T11:02:57Z

This branch fixes tm_data_table, tm_variable_browser and tm_missing_data modules to display the output on several cases.
In addition, the tm_front_page module was changed. With this branch, tm_front_page by default doesn't show the right-panel about the datasets.

tm_front_page

tm_front_page: pkgload::run_example("man/tm_front_page.Rd") displays the output without the right-panel.

The other modules

I tested the three modules and the example_module on the app.

Examples

Previously they did not show the output. Currently they do:

example_module: pkgload::run_example("../teal/man/example_module.Rd")displays the output
tm_data_table: pkgload::run_example("man/tm_data_table.Rd") displays the output.
tm_variable_browser: pkgload::run_example("man/tm_variable_browser.Rd") displays the output.
tm_missing_data: pkgload::run_example("man/tm_missing_data.Rd") displays the output.

`datanames = NULL`

Testing modules using datanames = "NULL" to disable the right-panel:

Code reprex

Code output:

Code:

library("teal")
devtools::load_all(".")

# general example data
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
  mtcars <- mtcars
  
  iris[] <- lapply(iris, add_nas)
  mtcars[] <- lapply(mtcars, add_nas)
  mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
  mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
})

datanames <- NULL
app <- init(
  data = data,
  modules = modules(
    example_module(datanames = datanames),
    tm_front_page(datanames = datanames),
    tm_data_table(datanames = datanames),
    tm_variable_browser(datanames = datanames),
    tm_missing_data(parent_dataname = "mtcars", datanames = datanames)
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

example_module: It doesn't show the right-panel
tm_front_page: It doesn't show the right-panel
tm_data_table: It doesn't show the right-panel
tm_variable_browser: It doesn't show the right-panel
tm_missing_data: It doesn't show the right-panel

From these modules only tm_missing_data has a parameter to pass transformers.
tm_missing_data with a transformer shows the right-panel with all the datasets:

tm_missing_data with transformer

Code output:

Code:

library("teal")
devtools::load_all(".")

# general example data
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
  mtcars <- mtcars
  
  iris[] <- lapply(iris, add_nas)
  mtcars[] <- lapply(mtcars, add_nas)
  mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
  mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
})

transf <- teal_transform_module(
  label = "Transformator",
  ui = function(id) {
    ns <- NS(id)
    tags$div(
      numericInput(ns("n_rows"), "Number of rows to subset", value = 32, min = 1, max = 150, step = 1)
    )
  },
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      reactive({
        within(data(),
               {
                 im_new <- head(iris, num_rows)
               },
               num_rows = input$n_rows
        )
      })
    })
  }
)

datanames <- NULL
app <- init(
  data = data,
  modules = modules(
    tm_missing_data(parent_dataname = "mtcars", transformators = list(transf), datanames = datanames)
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

`datanames = "all"`

Testing modules using datanames = "all" to show all the datasets on the right-panel:

Code

library("teal")
devtools::load_all(".")

# general example data
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
  mtcars <- mtcars
  
  iris[] <- lapply(iris, add_nas)
  mtcars[] <- lapply(mtcars, add_nas)
  mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
  mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
})

datanames <- "all"
app <- init(
  data = data,
  modules = modules(
    example_module(datanames = datanames),
    tm_front_page(datanames = datanames),
    tm_data_table(datanames = datanames),
    tm_variable_browser(datanames = datanames),
    tm_missing_data(parent_dataname = "mtcars", datanames = datanames)
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

example_module: It shows the right-panel
tm_front_page: It shows the right-panel
tm_data_table: It shows the right-panel
tm_variable_browser: It shows the right-panel
tm_missing_data: It shows the right-panel.

github-actions · 2025-01-24T15:16:49Z

Unit Tests Summary

1 files 22 suites 12m 59s ⏱️
145 tests 107 ✅ 38 💤 0 ❌
476 runs 438 ✅ 38 💤 0 ❌

Results for commit e9e1e1c.

♻️ This comment has been updated with latest results.

github-actions · 2025-01-24T15:16:52Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_pca	💚	$126.71$	$-8.35$	$0$	$0$	$0$	$0$
shinytest2-tm_a_regression	💚	$57.06$	$-5.12$	$0$	$0$	$0$	$0$
shinytest2-tm_data_table	💚	$20.50$	$-2.18$	$0$	$0$	$0$	$0$
shinytest2-tm_file_viewer	💚	$31.01$	$-2.41$	$0$	$0$	$0$	$0$
shinytest2-tm_g_association	💚	$34.29$	$-2.86$	$0$	$0$	$0$	$0$
shinytest2-tm_g_bivariate	💚	$78.70$	$-5.06$	$0$	$0$	$0$	$0$
shinytest2-tm_g_distribution	💚	$61.79$	$-4.09$	$0$	$0$	$0$	$0$
shinytest2-tm_g_response	💚	$31.89$	$-3.17$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplot	💚	$77.87$	$-4.95$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplotmatrix	💚	$29.80$	$-1.94$	$0$	$0$	$0$	$0$
shinytest2-tm_misssing_data	💚	$50.60$	$-2.55$	$0$	$0$	$0$	$0$
shinytest2-tm_outliers	💚	$119.09$	$-7.17$	$0$	$0$	$0$	$0$
shinytest2-tm_t_crosstable	💚	$33.95$	$-1.99$	$0$	$0$	$0$	$0$
shinytest2-tm_variable_browser	💚	$60.88$	$-4.77$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
shinytest2-tm_a_pca	💚	$9.13$	$-1.18$	e2e_tm_a_pca_Eigenvector_table_should_have_data_extract_selection_Murder_UrbanPop_on_header.
shinytest2-tm_a_regression	💚	$14.33$	$-1.49$	e2e_tm_a_regression_Plot_type_has_7_specific_choices_changing_choices_does_not_throw_errors.
shinytest2-tm_g_bivariate	💚	$28.28$	$-2.72$	e2e_tm_g_bivariate_Setting_encoding_inputs_produces_outputs_without_validation_errors.
shinytest2-tm_g_distribution	💚	$17.34$	$-1.83$	e2e_tm_g_distribution_Histogram_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_g_distribution	💚	$32.52$	$-1.30$	e2e_tm_g_distribution_Module_is_initialised_with_the_specified_defaults.
shinytest2-tm_g_response	💚	$13.57$	$-1.28$	e2e_tm_g_response_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_g_scatterplot	💚	$44.83$	$-2.36$	e2e_tm_g_scatterplot_The_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_outliers	💚	$18.01$	$-1.02$	e2e_tm_outliers_Plot_type_is_hidden_when_Boxplot_tab_is_not_selected.
shinytest2-tm_variable_browser	💚	$12.41$	$-1.33$	e2e_tm_variable_browser_changing_outlier_definition_encoding_doesn_t_show_errors.

Results for commit 3e1032a

♻️ This comment has been updated with latest results.

R/tm_front_page.R

m7pr

well done @llrs-roche

I tested the modules with your examples and everything looks fine and as expected. Left one comment about the extension of NEWS

llrs-roche added 4 commits January 21, 2025 15:56

Fix corner cases "all" and NULL

c134d2f

Invert the default to NULL instead of "all"

ff47c93

Work with datanames boundaries: "all" and NULL

91e686e

Update documentation

96ee564

llrs-roche added the core label Jan 22, 2025

llrs-roche added 2 commits January 24, 2025 12:04

Merged origin/main into 1452_datanames@main

fe758fc

Modify the app driver to match the previous behavior on test.

8bebda0

llrs-roche marked this pull request as ready for review January 24, 2025 14:43

github-actions bot added 2 commits January 24, 2025 14:45

[skip style] [skip vbump] Restyle files

ef074da

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

9e6e609

Merge branch 'main' into 1452_datanames@main

e9e1e1c

m7pr self-assigned this Jan 27, 2025

m7pr reviewed Jan 27, 2025

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llrs-roche merged commit ff4792f into main Jan 27, 2025

llrs-roche deleted the 1452_datanames@main branch January 27, 2025 15:11

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Display output on tm_data_table, tm_variable_browser, tm_missing_data#829

Display output on tm_data_table, tm_variable_browser, tm_missing_data#829
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tm_front_page

The other modules

Examples

datanames = NULL

datanames = "all"

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`datanames = NULL`

`datanames = "all"`

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