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🗃️ decorators feature branch #795

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@m7pr m7pr commented Nov 12, 2024 •
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Partner to insightsengineering/teal#1357
Introduces decorators to modules. More about decorators in here insightsengineering/teal#1384

Current working example for tm_a_regression 
devtools::load_all("../teal")
devtools::load_all(".")
footnote_regression <- teal_transform_module(
  server = make_teal_transform_server(expression(
    plot <- plot + labs(caption = deparse(summary(fit)[[1]]))
  ))
)

data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_a_regression(
      label = "Regression",
      response = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = "BMRKR1",
          selected = "BMRKR1",
          multiple = FALSE,
          fixed = TRUE
        )
      ),
      regressor = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variables:",
          choices = variable_choices(data[["ADSL"]], c("AGE", "SEX", "RACE")),
          selected = "AGE",
          multiple = TRUE,
          fixed = FALSE
        )
      ),
      decorators = list(footnote_regression)
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

@m7pr m7pr added the core label Nov 12, 2024
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@m7pr m7pr changed the title WIP for decorators feature Decorators feature Nov 19, 2024
@m7pr m7pr marked this pull request as ready for review November 19, 2024 11:08
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m7pr commented Nov 19, 2024

Marking this ready for the review, so we can start CI/CD tests

@m7pr m7pr changed the title Introduce decorators for tm_a_regression and tm_outliers introduce decorators for tm_a_regression Nov 20, 2024
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m7pr commented Nov 20, 2024

I moved tm_outliers to a separate PR #805

dependabot-preview bot and others added 9 commits November 20, 2024 14:04
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
3d48ec6
@m7pr
add req statement so that when srv_teal_transform_data returns NULL y…
4c4d214 
…ou see error from original teal_data
@github-actions
[skip style] [skip vbump] Restyle files
ce1ba17
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
6dcb2ef
@m7pr @averissimo
introduce decorators for tm_g_bivariate (#797)
cf4371f 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r
devtools::load_all("../teal")
devtools::load_all(".")
library(ggplot2)
interactive_decorator <- teal_transform_module(
  ui = function(id) {
    ns <- NS(id)
    div(
      textInput(ns("x_axis_title"), "X axis title", value = "x axis")
    )
  },
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      reactive({
        req(data())
        within(data(),
               {
                 plot <- plot +
                   xlab(my_title)
               },
               my_title = input$x_axis_title
        )
      })
    })
  }
)
# general data example
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  CO2 <- data.frame(CO2)
})

app <- init(
  data = data,
  modules = tm_g_bivariate(
    x = data_extract_spec(
      dataname = "CO2",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["CO2"]]),
        selected = "conc",
        fixed = FALSE
      )
    ),
    y = data_extract_spec(
      dataname = "CO2",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["CO2"]]),
        selected = "uptake",
        multiple = FALSE,
        fixed = FALSE
      )
    ),
    row_facet = data_extract_spec(
      dataname = "CO2",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["CO2"]]),
        selected = "Type",
        fixed = FALSE
      )
    ),
    col_facet = data_extract_spec(
      dataname = "CO2",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["CO2"]]),
        selected = "Treatment",
        fixed = FALSE
      )
    ),
    decorators = list(interactive_decorator)
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>

---------

Signed-off-by: Marcin <[email protected]>
Co-authored-by: André Veríssimo <[email protected]>
@averissimo
introduce decorators for tm_g_response (#802)
612bb06 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r
pkgload::load_all("../teal")
pkgload::load_all("../teal.modules.general")

footnote_dec <- teal_transform_module(
  label = "Footnote",
  ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = "I am a good decorator"),
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      logger::log_info("🟢 Footnote called to action!", namespace = "teal.modules.general")
      reactive(
        within(
          data(),
          {
            footnote_str <- footnote
            plot <- plot + ggplot2::labs(caption = footnote_str)
          },
          footnote = input$footnote
        )
      )
    })
  }
)


title_plot <- teal_transform_module(
  server = make_teal_transform_server(
    expression(
      logger::log_info("🔴 Title being called to action!", namespace = "teal.modules.general"),
      plot <- plot + ggplot2::ggtitle("A title to the plot")
    )
  )
)

# CDISC data example
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_g_response(
      label = "Response Plots",
      decorators = list(footnote_dec, title_plot),
      response = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], c("BMRKR2", "COUNTRY")),
          selected = "BMRKR2",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      x = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], c("SEX", "RACE")),
          selected = "RACE",
          multiple = FALSE,
          fixed = FALSE
        )
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>

---------

Signed-off-by: André Veríssimo <[email protected]>
@averissimo
introduce decorators for tm_g_distribution (#801)
006b374 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r
pkgload::load_all("../teal")
pkgload::load_all("../teal.modules.general")

footnote_dec <- teal_transform_module(
  label = "Footnote",
  ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = "I am a good decorator"),
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      logger::log_info("🟢 Footnote called to action!", namespace = "teal.modules.general")
      reactive(
        within(
          data(),
          {
            footnote_str <- footnote
            plot <- plot + ggplot2::labs(caption = footnote_str)
          },
          footnote = input$footnote
        )
      )
    })
  }
)

table_dup_dec <- teal_transform_module(
  server = make_teal_transform_server(
    expression(
      logger::log_info("🔴 Table dup being called to action!", namespace = "teal.modules.general"),
      summary_table <- rbind(summary_table, summary_table),
      if (exists("test_table")) test_table <- rbind(test_table, test_table, test_table) 
    )
  )
)

# CDISC data example
data <- teal_data()
data <- within(data, {
  ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

vars1 <- choices_selected(
  variable_choices(data[["ADSL"]], c("ARM", "COUNTRY", "SEX")),
  selected = NULL
)

app <- init(
  data = data,
  modules = modules(
    tm_g_distribution(
      decorators = list(footnote_dec, table_dup_dec),
      dist_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = variable_choices(data[["ADSL"]], c("AGE", "BMRKR1")),
          selected = "BMRKR1",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      strata_var = data_extract_spec(
        dataname = "ADSL",
        filter = filter_spec(
          vars = vars1,
          multiple = TRUE
        )
      ),
      group_var = data_extract_spec(
        dataname = "ADSL",
        filter = filter_spec(
          vars = vars1,
          multiple = TRUE
        )
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>

---------

Signed-off-by: André Veríssimo <[email protected]>
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@averissimo averissimo changed the title introduce decorators for tm_a_regression Feature branch: introduce decorators for tm_a_regression Nov 22, 2024
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g <- plot_call
print(g)
plot <- plot_call
print(plot)
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Need to move this later on

m7pr and others added 3 commits November 22, 2024 11:17
@m7pr @dependabot-preview @averissimo
introduce decorators for tm_t_crosstable (#806)
824efcf 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

````r
devtools::load_all("../teal")
devtools::load_all(".")


split_by_decorator <- teal_transform_module(
  label = "Footnote",
  ui = function(id) shiny::textInput(
    shiny::NS(id, "text"), "Insert row", "Hello World!" 
  ),
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      logger::log_info("🟢 Text called to action!", namespace = "teal.modules.general")
      reactive(
        within(
          data(),
          {
              table <- table %>% insert_rrow(rrow(text))
          },
          text = input$text
        )
      )
    })
  }
)

# CDISC data example
data <- teal_data()
data <- within(data, {
  ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_t_crosstable(
      label = "Cross Table",
      x = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], subset = function(data) {
            idx <- !vapply(data, inherits, logical(1), c("Date", "POSIXct", "POSIXlt"))
            return(names(data)[idx])
          }),
          selected = "COUNTRY",
          multiple = TRUE,
          ordered = TRUE,
          fixed = FALSE
        )
      ),
      y = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], subset = function(data) {
            idx <- vapply(data, is.factor, logical(1))
            return(names(data)[idx])
          }),
          selected = "SEX",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      decorators = list(split_by_decorator)
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}


````

</details>

---------

Signed-off-by: Marcin <[email protected]>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: André Veríssimo <[email protected]>
@m7pr @averissimo
introduce decorators for tm_a_pca (#798)
0fcddf0 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r

devtools::load_all("../teal")
devtools::load_all(".")
plot_title <- teal_transform_module(
  server = make_teal_transform_server(expression({
    plot <- plot + ggtitle("Custom title")
  }))
)

# general data example
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  USArrests <- USArrests
})

app <- init(
  data = data,
  modules = modules(
    tm_a_pca(
      "PCA",
      dat = data_extract_spec(
        dataname = "USArrests",
        select = select_spec(
          choices = variable_choices(
            data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
          ),
          selected = c("Murder", "Assault"),
          multiple = TRUE
        ),
        filter = NULL
      ),
      decorators = list(plot_title)
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

```

</details>

---------

Signed-off-by: Marcin <[email protected]>
Co-authored-by: André Veríssimo <[email protected]>
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
f915e29
@averissimo averissimo changed the title Feature branch: introduce decorators for tm_a_regression 🗃️ decorators feature branch Nov 22, 2024
averissimo and others added 10 commits November 22, 2024 12:24
@averissimo
chore: rename ui/srv_teal_transform_data to ui/srv_transform_teal_data
ba642f0
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
11d9ea8
@averissimo
fix: move print statement after decoration
5f2d532
@m7pr @averissimo
clean up print(plot) in tm_g_distribution module (#810)
89f1d44 
Signed-off-by: André Veríssimo <[email protected]>
Co-authored-by: André Veríssimo <[email protected]>
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
9375353
@m7pr @github-actions
@dependabot-preview @averissimo
introduce decorators for tm_g_scatterplotmatrix (#808)
09968a8 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r


pkgload::load_all("../teal")
pkgload::load_all(".")


footnote_dec <- teal_transform_module(
  label = "Footnote",
  ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = "I am a good decorator"),
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      logger::log_info("🟢 Footnote called to action!", namespace = "teal.modules.general")
      reactive(
        within(
          data(),
          {
            plot$xlab <- footnote
          },
          footnote = input$footnote
        )
      )
    })
  }
)

# general data example
data <- teal_data()
data <- within(data, {
  countries <- data.frame(
    id = c("DE", "FR", "IT", "ES", "PT", "GR", "NL", "BE", "LU", "AT"),
    government = factor(
      c(2, 2, 2, 1, 2, 2, 1, 1, 1, 2),
      labels = c("Monarchy", "Republic")
    ),
    language_family = factor(
      c(1, 3, 3, 3, 3, 2, 1, 1, 3, 1),
      labels = c("Germanic", "Hellenic", "Romance")
    ),
    population = c(83, 67, 60, 47, 10, 11, 17, 11, 0.6, 9),
    area = c(357, 551, 301, 505, 92, 132, 41, 30, 2.6, 83),
    gdp = c(3.4, 2.7, 2.1, 1.4, 0.3, 0.2, 0.7, 0.5, 0.1, 0.4),
    debt = c(2.1, 2.3, 2.4, 2.6, 2.3, 2.4, 2.3, 2.4, 2.3, 2.4)
  )
  sales <- data.frame(
    id = 1:50,
    country_id = sample(
      c("DE", "FR", "IT", "ES", "PT", "GR", "NL", "BE", "LU", "AT"),
      size = 50,
      replace = TRUE
    ),
    year = sort(sample(2010:2020, 50, replace = TRUE)),
    venue = sample(c("small", "medium", "large", "online"), 50, replace = TRUE),
    cancelled = sample(c(TRUE, FALSE), 50, replace = TRUE),
    quantity = rnorm(50, 100, 20),
    costs = rnorm(50, 80, 20),
    profit = rnorm(50, 20, 10)
  )
})
join_keys(data) <- join_keys(
  join_key("countries", "countries", "id"),
  join_key("sales", "sales", "id"),
  join_key("countries", "sales", c("id" = "country_id"))
)

app <- init(
  data = data,
  modules = modules(
    tm_g_scatterplotmatrix(
      label = "Scatterplot matrix",
      variables = list(
        data_extract_spec(
          dataname = "countries",
          select = select_spec(
            label = "Select variables:",
            choices = variable_choices(data[["countries"]]),
            selected = c("area", "gdp", "debt"),
            multiple = TRUE,
            ordered = TRUE,
            fixed = FALSE
          )
        ),
        data_extract_spec(
          dataname = "sales",
          filter = filter_spec(
            label = "Select variable:",
            vars = "country_id",
            choices = value_choices(data[["sales"]], "country_id"),
            selected = c("DE", "FR", "IT", "ES", "PT", "GR", "NL", "BE", "LU", "AT"),
            multiple = TRUE
          ),
          select = select_spec(
            label = "Select variables:",
            choices = variable_choices(data[["sales"]], c("quantity", "costs", "profit")),
            selected = c("quantity", "costs", "profit"),
            multiple = TRUE,
            ordered = TRUE,
            fixed = FALSE
          )
        )
      ),
      decorators = list(footnote_dec)
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: André Veríssimo <[email protected]>
@m7pr @averissimo
introduce decorators for tm_g_scatterplot (#807)
0870002 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r
pkgload::load_all("../teal")
pkgload::load_all(".")

footnote_dec <- teal_transform_module(
  label = "Footnote",
  ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = "I am a good decorator"),
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      logger::log_info("🟢 Footnote called to action!", namespace = "teal.modules.general")
      reactive(
        within(
          data(),
          {
            footnote_str <- footnote
            plot <- plot + ggplot2::labs(caption = footnote_str)
          },
          footnote = input$footnote
        )
      )
    })
  }
)

# CDISC data example
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_g_scatterplot(
      label = "Scatterplot Choices",
      x = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], c("AGE", "BMRKR1", "BMRKR2")),
          selected = "AGE",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      y = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], c("AGE", "BMRKR1", "BMRKR2")),
          selected = "BMRKR1",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color_by = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(
            data[["ADSL"]],
            c("AGE", "BMRKR1", "BMRKR2", "RACE", "REGION1")
          ),
          selected = NULL,
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      size_by = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], c("AGE", "BMRKR1")),
          selected = "AGE",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      row_facet = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], c("BMRKR2", "RACE", "REGION1")),
          selected = NULL,
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      col_facet = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["ADSL"]], c("BMRKR2", "RACE", "REGION1")),
          selected = NULL,
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      decorators = list(footnote_dec)
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

```

</details>

---------

Signed-off-by: Marcin <[email protected]>
Co-authored-by: André Veríssimo <[email protected]>
@m7pr @averissimo
introduce decorators for tm_g_association (#800)
b6ca759 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r

devtools::load_all("../teal")
devtools::load_all(".")
interactive_decorator <- teal_transform_module(
  ui = function(id) {
    ns <- NS(id)
    div(
      textInput(ns("x_axis_title_top"), "X axis title plot top", value = "x axis top"),
      textInput(ns("x_axis_title_bottom"), "X axis title plot bottom", value = "x axis bottom")
    )
  },
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      reactive({
        req(data())
        within(data(),
               {
                 plot_bottom <- plot_bottom + xlab(my_title_bottom)
                 plot_top <- plot_top + xlab(my_title_top)
               },
               my_title_top = input$x_axis_title_top,
               my_title_bottom = input$x_axis_title_bottom
        )
      })
    })
  }
)

# general data example
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  CO2 <- CO2
  factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L))))
  CO2[factors] <- lapply(CO2[factors], as.character)
})

app <- init(
  data = data,
  modules = modules(
    tm_g_association(
      ref = data_extract_spec(
        dataname = "CO2",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(data[["CO2"]], c("Plant", "Type", "Treatment")),
          selected = "Plant",
          fixed = FALSE
        )
      ),
      vars = data_extract_spec(
        dataname = "CO2",
        select = select_spec(
          label = "Select variables:",
          choices = variable_choices(data[["CO2"]], c("Plant", "Type", "Treatment")),
          selected = "Treatment",
          multiple = TRUE,
          fixed = FALSE
        )
      ),
      decorators = list(interactive_decorator)
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

```

</details>

---------

Co-authored-by: André Veríssimo <[email protected]>
@m7pr @averissimo
introduce decorators for tm_data_table (#799)
fb28571 
Part of insightsengineering/teal#1370

<details><summary> Working Example </summary>

```r


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

# general data example
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  iris <- iris
})

custom_table_decorator_interactive <- teal_transform_module(
  ui = function(id) {
    ns <- NS(id)
    div(
      selectInput(
        ns("style"), 
        "Table Style", 
        choices = c("Default", "Striped", "Hover"), 
        selected = "Default"
      )
    )
  },
  server = function(id, data) {
    moduleServer(id, function(input, output, session) {
      reactive({
        req(data(), input$style)
        within(data(), 
               {
                 if (style == "Striped") {
                   table <-
                     DT::formatStyle(
                       table,
                       columns = attr(table$x, "colnames")[-1],
                       target = 'row',
                       backgroundColor = '#f9f9f9'
                     )
                 } else if (style == "Hover") {
                   table <-
                     DT::formatStyle(
                       table,
                       columns = attr(table$x, "colnames")[-1],
                       target = 'row',
                       backgroundColor = '#f0f0f0'
                     )
                 }
               }, 
               style = input$style
        )
      })
    })
  }
)

app <- init(
  data = data,
  modules = modules(
    tm_data_table(
      variables_selected = list(
        iris = c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "Species")
      ),
      dt_args = list(caption = "IRIS Table Caption"),
      decorators = list(custom_table_decorator_interactive)
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>

---------

Signed-off-by: Marcin <[email protected]>
Co-authored-by: André Veríssimo <[email protected]>
@dependabot-preview
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
9ef1032
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@m7pr @averissimo @gogonzo @kpagacz