[Bug]: association module - `unused arguments (list(), "Race [RACE]")`

[m7pr]

Initially discovered during testing in here

#917 (comment)

[gogonzo]

Root problem is somewhere in a bivariate_plot_call when two categorical variables are selected. Module should work as follows:

• reference variable: single variable of any type.
• associated variable: multiple variables of any type.

Module should produce following plots:

• plot of reference variable "distribution" - for numeric a histogram, for categorical barplot with counts
• bivariate plot for each pair associated variable vs reference variable
  - numeric vs numeric: scatterplot
  - numeric vs categorical: boxplot
  - categorical vs categorical: mosaic plot

Bivariate app

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

app <- init(
  data = data,
  modules = tm_g_bivariate(
    x = data_extract_spec(
      dataname = "ADSL",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["ADSL"]]),
        selected = "ARM",
        fixed = FALSE
      )
    ),
    y = data_extract_spec(
      dataname = "ADSL",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["ADSL"]]),
        selected = "SEX",
        multiple = FALSE,
        fixed = FALSE
      )
    ),
    row_facet = data_extract_spec(
      dataname = "ADSL",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["ADSL"]]),
        selected = "ARM",
        fixed = FALSE
      )
    ),
    col_facet = data_extract_spec(
      dataname = "ADSL",
      select = select_spec(
        label = "Select variable:",
        choices = variable_choices(data[["ADSL"]]),
        selected = "COUNTRY",
        fixed = FALSE
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Association app

pkgload::load_all("teal.modules.general")
data <- teal_data()
data <- within(data, {
  require(nestcolor)
  ADSL <- teal.data::rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_g_association(
      ref = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variable:",
          choices = variable_choices(
            data[["ADSL"]],
            c("SEX", "RACE", "COUNTRY", "ARM", "STRATA1", "STRATA2", "ITTFL", "BMRKR2")
          ),
          selected = "RACE",
          fixed = FALSE
        )
      ),
      vars = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Select variables:",
          choices = variable_choices(
            data[["ADSL"]],
            c("SEX", "RACE", "COUNTRY", "ARM", "STRATA1", "STRATA2", "ITTFL", "BMRKR2")
          ),
          selected = "SEX",
          multiple = TRUE,
          fixed = FALSE
        )
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Closing: #919

[gogonzo]

Issue is related with haleyjeppson/ggmosaic#84
ggmosaic::geom_mosaic is used when plotting factor-vs-factor in bivariate (association-plot uses bivariate). Let's wait for estimates about ggmosaic's CRAN release. If failed, we can create geom_marimekko - but this is not a trivial task. It needs to use ggplot2::ggproto to properly draw the layer when facetting coloring etc.

[vedhav]

The tm_g_association tests were skipped here. Please un-skip them as part of this issue.