Spotfire POC

[gogonzo]

Fixes https://github.com/insightsengineering/coredev-tasks/issues/596

• POC example in inst/ directory
• Install dependencies:

remotes::install_github("insightsengineering/teal.widgets@spotfire_poc2")
remotes::install_github("insightsengineering/teal@spotfire_poc2")

example 1

pkgload::load_all("teal")
pkgload::load_all("teal.widgets")
pkgload::load_all("teal.modules.general")

# Example data
data <- within(teal_data(), {
  library(dplyr)
  library(tidyr)

  set.seed(123) # Setting a seed for reproducibility
  # Define possible maximum study days
  .possible_end_days <- c(50, 60, 70)

  # Create sample data
  synthetic_data <- tibble(subjid = c(1:15), strata = rep(c("category 1", "category 2"), length.out = 15)) |>
    rowwise() |>
    mutate(
      max_study_day = sample(.possible_end_days, 1),
      study_day = list(seq(10, max_study_day, by = 10))
    ) |>
    unnest(study_day) |>
    group_by(subjid) |>
    mutate(
      assigned_drug = sample(c("Drug A", "Drug B"), 1)
    ) |>
    ungroup() |>
    mutate(
      response_type = sample(c("CR", "PR"), n(), replace = TRUE),
      subjid = reorder(as.character(subjid), max_study_day)
    ) |>
    select(-max_study_day)
})

app <- init(
  data = data,
  modules = modules(
    tm_data_table(),
    tm_p_swimlane(
      label = "Swimlane",
      geom_specs = list(
        list(
          geom = str2lang("ggplot2::geom_col"),
          data = quote(synthetic_data),
          mapping = list(y = quote(subjid), x = quote(max(study_day))),
          width = 0.2
        ), # geom_col(data = synthetic_data, mapping = aes(x = subjid, x = max(study_day), width = 0.2)
        list(
          geom = quote(geom_point),
          data = quote(synthetic_data),
          mapping = list(
            y = quote(subjid), x = quote(study_day), color = quote(assigned_drug), shape = quote(assigned_drug)
          )
        ),
        list(
          geom = quote(geom_point),
          data = quote(synthetic_data),
          mapping = list(
            y = quote(subjid), x = quote(study_day), color = quote(response_type), shape = quote(response_type)
          )
        ),
        list(
          geom = quote(facet_wrap),
          facets = quote(vars(strata))
        )
      ),
      title = "Swimlane Efficacy Plot"
    )
  )
)

shinyApp(app$ui, app$server)

example adam

pkgload::load_all("teal")
pkgload::load_all("teal.widgets")
pkgload::load_all("teal.modules.general")

# Example data
data <- within(teal_data(), {
  library(dplyr)
  library(tidyr)
  ADSL <- teal.data::rADSL |> mutate(
    EOTSTT2 = case_when(
      !is.na(DCSREAS) ~ DCSREAS,
      TRUE ~ EOTSTT
    )
  )

  ADAE <- teal.data::rADAE
  ADRS <- teal.data::rADRS
})

join_keys(data) <- default_cdisc_join_keys

app <- init(
  data = data,
  modules = modules(
    tm_data_table(),
    tm_p_swimlane(
      label = "Swimlane",
      geom_specs = list(
        list(
          geom = quote(geom_col),
          data = quote(ADSL),
          mapping = list(y = quote(USUBJID), x = quote(EOSDY)),
          width = 0.2
        ), # geom_col(data = synthetic_data, mapping = aes(x = subjid, x = max(study_day), width = 0.2)
        list(
          geom = quote(geom_point),
          data = quote(ADSL),
          mapping = list(
            y = quote(USUBJID), x = quote(EOSDY), color = quote(EOTSTT2), shape = quote(EOTSTT2)
          )
        ),
        list(
          geom = quote(geom_point),
          data = quote(ADRS),
          mapping = list(
            y = quote(USUBJID), x = quote(ADY), color = quote(PARAMCD), shape = quote(PARAMCD)
          )
        ),
        list(
          geom = quote(geom_point),
          data = quote(ADAE),
          mapping = list(
            y = quote(USUBJID), x = quote(ASTDY), color = quote(AETERM), shape = quote(AETERM)
          )
        ),
        list(
          geom = quote(geom_point),
          data = quote(ADAE),
          mapping = list(
            y = quote(USUBJID), x = quote(AENDY), color = quote(AEOUT), shape = quote(AEOUT)
          )
        ),
        list(
          geom = quote(facet_grid),
          facets = quote(ARM ~ .),
          scales = "free"
        )
      ),
      title = "Swimlane Efficacy Plot"
    )
  )
)

shinyApp(app$ui, app$server)

[gogonzo]

At this moment we propose a very generic module which could be named tm_p_gglayers. Module can build any ggplot object bases on the list of specs provided through the module arguments. Please consider list below and see that list contain all informations necessary to create a ggplot layer.

list(
  geom = quote(geom_point),
  data = quote(synthetic_data),
  mapping = list(
    y = quote(subjid), x = quote(study_day), color = quote(assigned_drug), shape = quote(assigned_drug)
  )
)

# above is convertible:

geom_point(
  data = synthetic_data,
  mapping = aes(y = subjid, x = study_day, color = assigned_drug, shape = assigned_drug)
)

At this moment I was able to create such applications: