Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add decorators to all TMC modules #1371

Open
13 of 36 tasks
gogonzo opened this issue Oct 9, 2024 · 0 comments
Open
13 of 36 tasks

Add decorators to all TMC modules #1371

gogonzo opened this issue Oct 9, 2024 · 0 comments
Assignees
@averissimo @m7pr
Labels
core
Milestone
Decorate modules'...

Comments

@gogonzo
Copy link
Contributor

gogonzo commented Oct 9, 2024 •
edited by m7pr
Loading

Blocked by #1368

  • Assign yourself to a single module by adding your name next to the item.
  • add the decorator functionality to the module and update relevant documentation by including the decorator
  • Keep consistent output names - table, listing, graph
  • PR link should be added next to the item
  • once merged ✔️ the item

Items:

Part 1

Part 2

  • tm_t_binary_outcome
  • tm_t_coxreg
  • tm_t_events
  • tm_t_events_by_grade
  • tm_t_events_patyear
  • tm_t_events_summary
  • tm_t_exposure
  • tm_t_logistic
  • tm_t_mult_events
  • tm_t_pp_basic_info
  • tm_t_pp_laboratory
  • tm_t_pp_medical_history
  • tm_t_pp_prior_medication
  • tm_t_shift_by_arm
  • tm_t_shift_by_arm_by_worst
  • tm_t_shift_by_grade
  • tm_t_smq
  • tm_t_summary
  • tm_t_summary_by
  • tm_t_tte
@gogonzo gogonzo added this to the Decorate modules' output milestone Oct 9, 2024
@gogonzo gogonzo added the core label Oct 9, 2024
@averissimo averissimo mentioned this issue Nov 25, 2024
Open
This was referenced Nov 26, 2024
Merged
Merged
Merged
Merged
@llrs-roche llrs-roche mentioned this issue Nov 27, 2024
Closed
This was referenced Nov 27, 2024
Merged
Merged
Merged
Merged
Merged
This was referenced Nov 28, 2024
Merged
Merged
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 28, 2024
@llrs-roche @m7pr
introduce decorators for tm_g_ci (#1265)
b565310 
Part of insightsengineering/teal#1371

WIP

<details>
<summary> Example with decorator </summary>

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

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

caption_decorator <- function(default_caption = "I am a good decorator", .var_to_replace = "plot") {
  teal_transform_module(
    label = "Caption",
    ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::labs(caption = footnote)
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}



app <- init(
  data = data,
  modules = modules(
    tm_g_ci(
      label = "Confidence Interval Plot",
      x_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = c("ARMCD", "BMRKR2"),
          selected = c("ARMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      y_var = data_extract_spec(
        dataname = "ADLB",
        filter = list(
          filter_spec(
            vars = "PARAMCD",
            choices = levels(ADLB$PARAMCD),
            selected = levels(ADLB$PARAMCD)[1],
            multiple = FALSE,
            label = "Select lab:"
          ),
          filter_spec(
            vars = "AVISIT",
            choices = levels(ADLB$AVISIT),
            selected = levels(ADLB$AVISIT)[1],
            multiple = FALSE,
            label = "Select visit:"
          )
        ),
        select = select_spec(
          label = "Analyzed Value",
          choices = c("AVAL", "CHG"),
          selected = "AVAL",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Color by variable",
          choices = c("SEX", "STRATA1", "STRATA2"),
          selected = c("STRATA1"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      decorators = list(caption_decorator(.var_to_replace = "plot"))
    )
  )
)
shinyApp(app$ui, app$server)
```

</details>

---------

Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com>
Co-authored-by: m7pr <marcin.kosinski.mk1@roche.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 28, 2024
@llrs-roche @m7pr
Introduce decorators to tm_g_forest_rsp (#1266)
2276fca 
Part of insightsengineering/teal#1371

This module also returns a plot from `cowplot`, and I am not sure if the
example I got works well (I am not that familiar with it).

<details>
<summary>Draft of an example</summary>

````r
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")
library(nestcolor)
library(dplyr)

caption_decorator <- function(annotation = "I am a good decorator", var_to_decorate = "plot") {
  teal_transform_module(
    label = "Annotation",
    ui = function(id) shiny::textInput(shiny::NS(id, "annotation"), "Annotation", value = annotation),
    server = make_teal_transform_server(
      substitute({
        var_to_decorate <- cowplot::add_sub(var_to_decorate, annotation)
      }, env = list(var_to_decorate = as.name(var_to_decorate)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADRS <- tmc_ex_adrs %>%
    mutate(AVALC = d_onco_rsp_label(AVALC) %>%
             with_label("Character Result/Finding")) %>%
    filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADRS <- data[["ADRS"]]

arm_ref_comp <- list(
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  ),
  ARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  )
)

app <- init(
  data = data,
  modules = modules(
    tm_g_forest_rsp(
      label = "Forest Response",
      dataname = "ADRS",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADRS, "PARAMCD", "PARAM"),
        "INVET"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      ),
      plot_height = c(600L, 200L, 2000L),
      default_responses = list(
        BESRSPI = list(
          rsp = c("Stable Disease (SD)", "Not Evaluable (NE)"),
          levels = c(
            "Complete Response (CR)", "Partial Response (PR)", "Stable Disease (SD)",
            "Progressive Disease (PD)", "Not Evaluable (NE)"
          )
        ),
        INVET = list(
          rsp = c("Complete Response (CR)", "Partial Response (PR)"),
          levels = c(
            "Complete Response (CR)", "Not Evaluable (NE)", "Partial Response (PR)",
            "Progressive Disease (PD)", "Stable Disease (SD)"
          )
        ),
        OVRINV = list(
          rsp = c("Progressive Disease (PD)", "Stable Disease (SD)"),
          levels = c("Progressive Disease (PD)", "Stable Disease (SD)", "Not Evaluable (NE)")
        )
      ),
      decorators = list(caption_decorator())
    )
  )
)
shinyApp(app$ui, app$server)


```

</details>

---------

Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com>
Co-authored-by: m7pr <marcin.kosinski.mk1@roche.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 28, 2024
@m7pr
introduce decorators for tm_g_forest_tte (#1264)
fd17aed 
Part of insightsengineering/teal#1371

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

```r
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")
library(nestcolor)
library(dplyr)

caption_decorator <- function(annotation = "I am a good decorator", var_to_decorate = "plot") {
  teal_transform_module(
    label = "Annotation",
    ui = function(id) shiny::textInput(shiny::NS(id, "annotation"), "Annotation", value = annotation),
    server = make_teal_transform_server(
      substitute({
        var_to_decorate <- cowplot::add_sub(var_to_decorate, annotation)
      }, env = list(var_to_decorate = as.name(var_to_decorate)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADTTE <- tmc_ex_adtte
  ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADTTE <- data[["ADTTE"]]

arm_ref_comp <- list(
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  ),
  ARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  )
)

app <- init(
  data = data,
  modules = modules(
    tm_g_forest_tte(
      label = "Forest Survival",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      ),
      decorators = list(caption_decorator())
    )
  )
)
shinyApp(app$ui, app$server)


```

</details>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 28, 2024
@m7pr
introduce decorators for tm_a_gee (#1262)
4e747f9 
Part of insightsengineering/teal#1371

Alternative to
#1259

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

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

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New row",
    ui = function(id) shiny::textInput(shiny::NS(id, "new_row"), "New row", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- rtables::insert_rrow(.var_to_replace, rtables::rrow(new_row))
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADQS <- tmc_ex_adqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor(),
      AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
    ) %>%
    droplevels()
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_a_gee(
      label = "GEE",
      dataname = "ADQS",
      aval_var = choices_selected("AVALBIN", fixed = TRUE),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      paramcd = choices_selected(
        choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
      decorators = list(insert_rrow_decorator("Hello world", "table"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}


```

</details>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 28, 2024
@m7pr
introduce decorators for tm_g_ipp (#1263)
fcc3682 
Part of insightsengineering/teal#1371

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

```r

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

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl %>%
    slice(1:20) %>%
    df_explicit_na()
  ADLB <- tmc_ex_adlb %>%
    filter(USUBJID %in% ADSL$USUBJID) %>%
    df_explicit_na() %>%
    filter(AVISIT != "SCREENING")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

caption_decorator <- function(default_caption = "I am a good decorator", .var_to_replace = "plot") {
  teal_transform_module(
    label = "Caption",
    ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::labs(caption = footnote)
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_ipp(
      label = "Individual Patient Plot",
      dataname = "ADLB",
      arm_var = choices_selected(
        value_choices(ADLB, "ARMCD"),
        "ARM A"
      ),
      paramcd = choices_selected(
        value_choices(ADLB, "PARAMCD"),
        "ALT"
      ),
      aval_var = choices_selected(
        variable_choices(ADLB, c("AVAL", "CHG")),
        "AVAL"
      ),
      avalu_var = choices_selected(
        variable_choices(ADLB, c("AVALU")),
        "AVALU",
        fixed = TRUE
      ),
      id_var = choices_selected(
        variable_choices(ADLB, c("USUBJID")),
        "USUBJID",
        fixed = TRUE
      ),
      visit_var = choices_selected(
        variable_choices(ADLB, c("AVISIT")),
        "AVISIT"
      ),
      baseline_var = choices_selected(
        variable_choices(ADLB, c("BASE")),
        "BASE",
        fixed = TRUE
      ),
      add_baseline_hline = FALSE,
      separate_by_obs = FALSE,
      decorators = list(caption_decorator(.var_to_replace = "plot"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

```

</details>
This was referenced Nov 28, 2024
Open
Merged
Open
@llrs-roche llrs-roche mentioned this issue Nov 28, 2024
Merged
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@llrs-roche @m7pr
introduce decorators to tm_g_pp_patient_timeline (#1270)
98520eb 
Part of insightsengineering/teal#1371

<details>
<summary>Example using cowplot::add_sub with ggplot2</summary>

```r
devtools::load_all("../teal.modules.general")
devtools::load_all("../teal.reporter")
devtools::load_all("../teal")
devtools::load_all(".")
library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADAE <- tmc_ex_adae
  ADSL <- tmc_ex_adsl %>%
    filter(USUBJID %in% ADAE$USUBJID)
  ADCM <- tmc_ex_adcm %>%
    mutate(
      CMSTDY = case_when(
        CMCAT == "medcl B" ~ 20,
        CMCAT == "medcl C" ~ 150,
        TRUE ~ 1
      ) %>% with_label("Study Day of Start of Medication"),
      CMENDY = case_when(
        CMCAT == "medcl B" ~ 700,
        CMCAT == "medcl C" ~ 1000,
        TRUE ~ 500
      ) %>% with_label("Study Day of End of Medication"),
      CMASTDTM = ASTDTM,
      CMAENDTM = AENDTM
    )
})

join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADAE", "ADCM")]
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys
join_keys(data)["ADAE", "ADCM"] <- c("STUDYID", "USUBJID")


caption_decorator <- function(annotation = "I am a good decorator", var_to_decorate = "plot") {
  teal_transform_module(
    label = "Annotation",
    ui = function(id) shiny::textInput(shiny::NS(id, "annotation"), "Annotation", value = annotation),
    server = make_teal_transform_server(
      substitute({
        var_to_decorate <- cowplot::add_sub(var_to_decorate, annotation)
      }, env = list(var_to_decorate = as.name(var_to_decorate)))
    )
  )
}


app <- init(
  data = data,
  modules = modules(
    tm_g_pp_patient_timeline(
      label = "Patient Timeline",
      dataname_adae = "ADAE",
      dataname_adcm = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      cmdecod = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMDECOD"),
        selected = "CMDECOD",
      ),
      aeterm = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AETERM"),
        selected = c("AETERM")
      ),
      aetime_start = choices_selected(
        choices = variable_choices(data[["ADAE"]], "ASTDTM"),
        selected = c("ASTDTM")
      ),
      aetime_end = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AENDTM"),
        selected = c("AENDTM")
      ),
      dstime_start = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMASTDTM"),
        selected = c("CMASTDTM")
      ),
      dstime_end = choices_selected(
        choices = variable_choices(data[["ADCM"]], "CMAENDTM"),
        selected = c("CMAENDTM")
      ),
      aerelday_start = choices_selected(
        choices = variable_choices(data[["ADAE"]], "ASTDY"),
        selected = c("ASTDY")
      ),
      aerelday_end = choices_selected(
        choices = variable_choices(data[["ADAE"]], "AENDY"),
        selected = c("AENDY")
      ),
      dsrelday_start = choices_selected(
        choices = variable_choices(data[["ADCM"]], "ASTDY"),
        selected = c("ASTDY")
      ),
      dsrelday_end = choices_selected(
        choices = variable_choices(data[["ADCM"]], "AENDY"),
        selected = c("AENDY")
      ),
      decorators = list(caption_decorator())
    )
  )
)
shinyApp(app$ui, app$server)
```

</details>

---------

Co-authored-by: m7pr <marcin.kosinski.mk1@roche.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@m7pr
introduce decorators for tm_g_pp_therapy (#1268)
f462d60 
Part of insightsengineering/teal#1371

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

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

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADCM <- tmc_ex_adcm
  ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)
  ADCM$CMASTDTM <- ADCM$ASTDTM
  ADCM$CMAENDTM <- ADCM$AENDTM
})

join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADCM")]
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys

ADSL <- data[["ADSL"]]
ADCM <- data[["ADCM"]]

caption_decorator <- function(default_caption = "I am a good decorator", .var_to_replace = "plot") {
  teal_transform_module(
    label = "Caption",
    ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::labs(caption = footnote)
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

head_decorator <- function(default_value = 6, .var_to_replace = "object") {
  teal_transform_module(
    label = "Head",
    ui = function(id) shiny::numericInput(shiny::NS(id, "n"), "N rows", value = default_value),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- utils::head(.var_to_replace, n = n)
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_pp_therapy(
      label = "Therapy",
      dataname = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      atirel = choices_selected(
        choices = variable_choices(ADCM, "ATIREL"),
        selected = c("ATIREL")
      ),
      cmdecod = choices_selected(
        choices = variable_choices(ADCM, "CMDECOD"),
        selected = "CMDECOD"
      ),
      cmindc = choices_selected(
        choices = variable_choices(ADCM, "CMINDC"),
        selected = "CMINDC"
      ),
      cmdose = choices_selected(
        choices = variable_choices(ADCM, "CMDOSE"),
        selected = "CMDOSE"
      ),
      cmtrt = choices_selected(
        choices = variable_choices(ADCM, "CMTRT"),
        selected = "CMTRT"
      ),
      cmdosu = choices_selected(
        choices = variable_choices(ADCM, "CMDOSU"),
        selected = c("CMDOSU")
      ),
      cmroute = choices_selected(
        choices = variable_choices(ADCM, "CMROUTE"),
        selected = "CMROUTE"
      ),
      cmdosfrq = choices_selected(
        choices = variable_choices(ADCM, "CMDOSFRQ"),
        selected = "CMDOSFRQ"
      ),
      cmstdy = choices_selected(
        choices = variable_choices(ADCM, "ASTDY"),
        selected = "ASTDY"
      ),
      cmendy = choices_selected(
        choices = variable_choices(ADCM, "AENDY"),
        selected = "AENDY"
      ),
      decorators = list(plot = caption_decorator('Marcin', 'plot'), table = head_decorator(2, 'table'))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@m7pr @averissimo
introduce decorators for tm_g_pp_vitals (#1261)
3ae43d2 
Part of insightsengineering/teal#1371

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

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

library(nestcolor)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADVS <- tmc_ex_advs
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADVS <- data[["ADVS"]]

change_theme_decorator <- function(default_check = TRUE, .var_to_replace = "plot") {
  teal_transform_module(
    label = "Theme",
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::theme_void()
      }, 
      env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_pp_vitals(
      label = "Vitals",
      dataname = "ADVS",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      paramcd = choices_selected(
        choices = variable_choices(ADVS, "PARAMCD"),
        selected = "PARAMCD"
      ),
      xaxis = choices_selected(
        choices = variable_choices(ADVS, "ADY"),
        selected = "ADY"
      ),
      aval_var = choices_selected(
        choices = variable_choices(ADVS, "AVAL"),
        selected = "AVAL"
      )#,
      #decorators = list(plot = change_theme_decorator(TRUE, "plot"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}devtools::load_all("../teal")
devtools::load_all(".")

library(nestcolor)
library(dplyr)
library(forcats)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb %>%
    mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

change_theme_decorator <- function(default_check = TRUE, .var_to_replace = "plot") {
  teal_transform_module(
    label = "Theme",
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::theme_void()
      }, 
      env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_lineplot(
      label = "Line Plot",
      dataname = "ADLB",
      strata = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      y = choices_selected(
        variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
        "AVAL"
      ),
      param = choices_selected(
        value_choices(ADLB, "PARAMCD", "PARAM"),
        "ALT"
      ),
      decorators = list(plot = change_theme_decorator(TRUE, "plot"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>

---------

Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@m7pr @llrs-roche @averissimo
introduce decorators for tm_t_abnormality (#1257)
d7b036e 
Part of insightsengineering/teal#1371

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

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

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New row",
    ui = function(id) shiny::textInput(shiny::NS(id, "new_row"), "New row", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- rtables::insert_rrow(.var_to_replace, rtables::rrow(new_row))
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb %>%
    mutate(
      ONTRTFL = case_when(
        AVISIT %in% c("SCREENING", "BASELINE") ~ "",
        TRUE ~ "Y"
      ) %>% with_label("On Treatment Record Flag")
    )
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_abnormality(
      label = "Abnormality Table",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      add_total = FALSE,
      by_vars = choices_selected(
        choices = variable_choices(ADLB, subset = c("LBCAT", "PARAM", "AVISIT")),
        selected = c("LBCAT", "PARAM"),
        keep_order = TRUE
      ),
      baseline_var = choices_selected(
        variable_choices(ADLB, subset = "BNRIND"),
        selected = "BNRIND", fixed = TRUE
      ),
      grade = choices_selected(
        choices = variable_choices(ADLB, subset = "ANRIND"),
        selected = "ANRIND",
        fixed = TRUE
      ),
      abnormal = list(low = "LOW", high = "HIGH"),
      exclude_base_abn = FALSE,
      decorators = list(insert_rrow_decorator("I am a good new row"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

```

</details>

---------

Co-authored-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@m7pr @averissimo
Introduce decorators for tm_g_km (#1254)
af7ecff 
Part of insightsengineering/teal#1371

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

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

library(nestcolor)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADTTE <- tmc_ex_adtte
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADTTE <- data[["ADTTE"]]

arm_ref_comp <- list(
  ACTARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  ),
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  )
)

change_theme_decorator <- function(default_check = TRUE, .var_to_replace = "plot") {
  teal_transform_module(
    label = "Theme",
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::theme_void()
      }, 
      env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_km(
      label = "Kaplan-Meier Plot",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      arm_ref_comp = arm_ref_comp,
      strata_var = choices_selected(
        variable_choices(ADSL, c("SEX", "BMRKR2")),
        "SEX"
      ),
      facet_var = choices_selected(
        variable_choices(ADSL, c("SEX", "BMRKR2")),
        NULL
      ),
      decorators = list(plot = change_theme_decorator(TRUE, "plot"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}


```

</details>

---------

Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@m7pr @averissimo
Introduce decorators for tm_g_lineplot (#1255)
078fc51 
Part of insightsengineering/teal#1371

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

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

library(nestcolor)
library(dplyr)
library(forcats)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb %>%
    mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

change_theme_decorator <- function(default_check = TRUE, .var_to_replace = "plot") {
  teal_transform_module(
    label = "Theme",
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::theme_void()
      }, 
      env = list(.var_to_replace = as.name(.var_to_replace))
      )
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_lineplot(
      label = "Line Plot",
      dataname = "ADLB",
      strata = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      y = choices_selected(
        variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
        "AVAL"
      ),
      param = choices_selected(
        value_choices(ADLB, "PARAMCD", "PARAM"),
        "ALT"
      ),
      decorators = list(plot = change_theme_decorator(TRUE, "plot"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}
```

</details>

---------

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@m7pr @averissimo @llrs-roche
introduce decorators for tm_t_ancova (#1256)
dab7f4e 
Part of insightsengineering/teal#1371

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

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

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New row",
    ui = function(id) shiny::textInput(shiny::NS(id, "new_row"), "New row", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- rtables::insert_rrow(.var_to_replace, rtables::rrow(new_row))
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADQS <- tmc_ex_adqs
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADQS <- data[["ADQS"]]

arm_ref_comp <- list(
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  ),
  ACTARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  )
)

app <- init(
  data = data,
  modules = modules(
    tm_t_ancova(
      label = "ANCOVA Table",
      dataname = "ADQS",
      avisit = choices_selected(
        choices = value_choices(ADQS, "AVISIT"),
        selected = "WEEK 1 DAY 8"
      ),
      arm_var = choices_selected(
        choices = variable_choices(ADSL, c("ARM", "ACTARMCD", "ARMCD")),
        selected = "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      aval_var = choices_selected(
        choices = variable_choices(ADQS, c("CHG", "AVAL")),
        selected = "CHG"
      ),
      cov_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADQS, "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      interact_var = choices_selected(
        choices = variable_choices(ADQS, c("BASE", "STRATA1", "SEX")),
        selected = "STRATA1"
      ),
      decorators = list(insert_rrow_decorator("I am a good new row"))
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}





```

</details>

---------

Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Co-authored-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
m7pr added a commit to insightsengineering/teal.modules.clinical that referenced this issue Nov 29, 2024
@m7pr @llrs-roche
introduce decorators for tm_t_abnormality_by_worst_grade (#1260)
e3bc080 
Part of insightsengineering/teal#1371

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

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

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New row",
    ui = function(id) shiny::textInput(shiny::NS(id, "new_row"), "New row", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- rtables::insert_rrow(.var_to_replace, rtables::rrow(new_row))
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}


library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb %>%
    filter(!AVISIT %in% c("SCREENING", "BASELINE"))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_abnormality_by_worst_grade(
      label = "Laboratory Test Results with Highest Grade Post-Baseline",
      dataname = "ADLB",
      arm_var = choices_selected(
        choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        choices = value_choices(ADLB, "PARAMCD", "PARAM"),
        selected = c("ALT", "CRP", "IGA")
      ),
      add_total = FALSE,
      decorators = list(insert_rrow_decorator("I am a good new row"))
    )
  ),
  filter = teal_slices(
    teal_slice("ADSL", "SAFFL", selected = "Y"),
    teal_slice("ADLB", "ONTRTFL", selected = "Y")
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

```

</details>

---------

Co-authored-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@averissimo averissimo

@m7pr m7pr

Labels
core
Projects
None yet
Milestone
Decorate modules' output
Development

No branches or pull requests
3 participants
@averissimo @gogonzo @m7pr