introduce decorators to `tm_g_pp_patient_timeline` #1270

llrs-roche · 2024-11-28T17:26:00Z

Example using cowplot::add_sub with ggplot2

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)

…ent place

llrs-roche · 2024-11-29T09:16:24Z

In this module I wasn't sure where to place the decorator. I end up deciding to put it on the last element of the fixed input. Below there are some input forms that might change. I think this will make it more stable for user but it might not be consistent with other modules that also have conditional inputs

m7pr · 2024-11-29T09:37:00Z

When running the code I see below in the console. This is most probably from print(plot)
that gets passed to srv_decorate_teal_data that goes

eval_code(decorated_output(), expr)

Have you seen this in other modules that you did/review?

> shinyApp(app$ui, app$server)

Listening on http://127.0.0.1:3885
TableGrob (19 x 14) "layout": 24 grobs
    z         cells             name
1   0 ( 1-19, 1-14)       background
2   1 ( 9- 9, 7- 7)        panel-1-1
3   1 (11-11, 7- 7)        panel-2-1
4   3 ( 8- 8, 7- 7)         axis-t-1
5   3 (12-12, 7- 7)         axis-b-1
6   3 ( 9- 9, 6- 6)         axis-l-1
7   3 (11-11, 6- 6)         axis-l-2
8   3 ( 9- 9, 9- 9)         axis-r-1
9   3 (11-11, 9- 9)         axis-r-2
10  2 ( 9- 9, 8- 8)        strip-r-1
11  2 (11-11, 8- 8)        strip-r-2
12  4 ( 7- 7, 7- 7)           xlab-t
13  5 (13-13, 7- 7)           xlab-b
14  6 ( 9-11, 5- 5)           ylab-l
15  7 ( 9-11,10-10)           ylab-r
16  8 ( 9-11,12-12)  guide-box-right
17  9 ( 9-11, 3- 3)   guide-box-left
18 10 (15-15, 7- 7) guide-box-bottom
19 11 ( 5- 5, 7- 7)    guide-box-top
20 12 ( 9-11, 7- 7) guide-box-inside
21 13 ( 4- 4, 7- 7)         subtitle
22 14 ( 3- 3, 7- 7)            title
23 15 (16-16, 7- 7)          caption
24 16 (17-17, 7- 7)              sub
                                            grob
1                rect[plot.background..rect.237]
2                       gTree[panel-1.gTree.175]
3                       gTree[panel-2.gTree.185]
4                                 zeroGrob[NULL]
5            absoluteGrob[GRID.absoluteGrob.190]
6            absoluteGrob[GRID.absoluteGrob.195]
7            absoluteGrob[GRID.absoluteGrob.200]
8                                 zeroGrob[NULL]
9                                 zeroGrob[NULL]
10                                 gtable[strip]
11                                 gtable[strip]
12                                zeroGrob[NULL]
13 titleGrob[axis.title.x.bottom..titleGrob.227]
14   titleGrob[axis.title.y.left..titleGrob.230]
15                                zeroGrob[NULL]
16                                zeroGrob[NULL]
17                                zeroGrob[NULL]
18                                zeroGrob[NULL]
19                                zeroGrob[NULL]
20                                zeroGrob[NULL]
21         zeroGrob[plot.subtitle..zeroGrob.234]
22          titleGrob[plot.title..titleGrob.233]
23          zeroGrob[plot.caption..zeroGrob.235]
24                           text[GRID.text.163]
TableGrob (19 x 14) "layout": 24 grobs
    z         cells             name
1   0 ( 1-19, 1-14)       background
2   1 ( 9- 9, 7- 7)        panel-1-1
3   1 (11-11, 7- 7)        panel-2-1
4   3 ( 8- 8, 7- 7)         axis-t-1
5   3 (12-12, 7- 7)         axis-b-1
6   3 ( 9- 9, 6- 6)         axis-l-1
7   3 (11-11, 6- 6)         axis-l-2
8   3 ( 9- 9, 9- 9)         axis-r-1
9   3 (11-11, 9- 9)         axis-r-2
10  2 ( 9- 9, 8- 8)        strip-r-1
11  2 (11-11, 8- 8)        strip-r-2
12  4 ( 7- 7, 7- 7)           xlab-t
13  5 (13-13, 7- 7)           xlab-b
14  6 ( 9-11, 5- 5)           ylab-l
15  7 ( 9-11,10-10)           ylab-r
16  8 ( 9-11,12-12)  guide-box-right
17  9 ( 9-11, 3- 3)   guide-box-left
18 10 (15-15, 7- 7) guide-box-bottom
19 11 ( 5- 5, 7- 7)    guide-box-top
20 12 ( 9-11, 7- 7) guide-box-inside
21 13 ( 4- 4, 7- 7)         subtitle
22 14 ( 3- 3, 7- 7)            title
23 15 (16-16, 7- 7)          caption
24 16 (17-17, 7- 7)              sub
                                            grob
1                rect[plot.background..rect.312]
2                       gTree[panel-1.gTree.250]
3                       gTree[panel-2.gTree.260]
4                                 zeroGrob[NULL]
5            absoluteGrob[GRID.absoluteGrob.265]
6            absoluteGrob[GRID.absoluteGrob.270]
7            absoluteGrob[GRID.absoluteGrob.275]
8                                 zeroGrob[NULL]
9                                 zeroGrob[NULL]
10                                 gtable[strip]
11                                 gtable[strip]
12                                zeroGrob[NULL]
13 titleGrob[axis.title.x.bottom..titleGrob.302]
14   titleGrob[axis.title.y.left..titleGrob.305]
15                                zeroGrob[NULL]
16                                zeroGrob[NULL]
17                                zeroGrob[NULL]
18                                zeroGrob[NULL]
19                                zeroGrob[NULL]
20                                zeroGrob[NULL]
21         zeroGrob[plot.subtitle..zeroGrob.309]
22          titleGrob[plot.title..titleGrob.308]
23          zeroGrob[plot.caption..zeroGrob.310]
24                           text[GRID.text.238]
TableGrob (19 x 14) "layout": 24 grobs
    z         cells             name
1   0 ( 1-19, 1-14)       background
2   1 ( 9- 9, 7- 7)        panel-1-1
3   1 (11-11, 7- 7)        panel-2-1
4   3 ( 8- 8, 7- 7)         axis-t-1
5   3 (12-12, 7- 7)         axis-b-1
6   3 ( 9- 9, 6- 6)         axis-l-1
7   3 (11-11, 6- 6)         axis-l-2
8   3 ( 9- 9, 9- 9)         axis-r-1
9   3 (11-11, 9- 9)         axis-r-2
10  2 ( 9- 9, 8- 8)        strip-r-1
11  2 (11-11, 8- 8)        strip-r-2
12  4 ( 7- 7, 7- 7)           xlab-t
13  5 (13-13, 7- 7)           xlab-b
14  6 ( 9-11, 5- 5)           ylab-l
15  7 ( 9-11,10-10)           ylab-r
16  8 ( 9-11,12-12)  guide-box-right
17  9 ( 9-11, 3- 3)   guide-box-left
18 10 (15-15, 7- 7) guide-box-bottom
19 11 ( 5- 5, 7- 7)    guide-box-top
20 12 ( 9-11, 7- 7) guide-box-inside
21 13 ( 4- 4, 7- 7)         subtitle
22 14 ( 3- 3, 7- 7)            title
23 15 (16-16, 7- 7)          caption
24 16 (17-17, 7- 7)              sub
                                            grob
1                rect[plot.background..rect.387]
2                       gTree[panel-1.gTree.325]
3                       gTree[panel-2.gTree.335]
4                                 zeroGrob[NULL]
5            absoluteGrob[GRID.absoluteGrob.340]
6            absoluteGrob[GRID.absoluteGrob.345]
7            absoluteGrob[GRID.absoluteGrob.350]
8                                 zeroGrob[NULL]
9                                 zeroGrob[NULL]
10                                 gtable[strip]
11                                 gtable[strip]
12                                zeroGrob[NULL]
13 titleGrob[axis.title.x.bottom..titleGrob.377]
14   titleGrob[axis.title.y.left..titleGrob.380]
15                                zeroGrob[NULL]
16                                zeroGrob[NULL]
17                                zeroGrob[NULL]
18                                zeroGrob[NULL]
19                                zeroGrob[NULL]
20                                zeroGrob[NULL]
21         zeroGrob[plot.subtitle..zeroGrob.384]
22          titleGrob[plot.title..titleGrob.383]
23          zeroGrob[plot.caption..zeroGrob.385]
24                           text[GRID.text.313]

llrs-roche · 2024-11-29T09:39:24Z

I just started seeing this today, but only when there was an issue with the module if my memory serves me well.

R/tm_g_pp_patient_timeline.R

…ttps://github.com/insightsengineering/teal.modules.clinical into tm_g_pp_patient_timeline@1187_decorate_output@main

introduce decorators to tm_g_pp_patient_timeline

8942d31

llrs-roche added the core label Nov 28, 2024

llrs-roche mentioned this pull request Nov 29, 2024

Add decorators to all TMC modules insightsengineering/teal#1371

Closed

36 tasks

llrs-roche added 4 commits November 29, 2024 10:05

Adding missing decorator checks and moving the decorators to a differ…

6bfd357

…ent place

fix mistake

5e73bbe

Rename variable

87b7b67

Fix mistake

d3f2c50

llrs-roche marked this pull request as ready for review November 29, 2024 09:14

move ui so it is more consitent with other modules

0cd5b4a

m7pr reviewed Nov 29, 2024

View reviewed changes

R/tm_g_pp_patient_timeline.R Outdated Show resolved Hide resolved

llrs-roche added 2 commits November 29, 2024 10:44

Fix issue with messages on the console about the plot

c8b883e

Merge branch 'tm_g_pp_patient_timeline@1187_decorate_output@main' of h…

f743995

…ttps://github.com/insightsengineering/teal.modules.clinical into tm_g_pp_patient_timeline@1187_decorate_output@main

m7pr self-assigned this Nov 29, 2024

m7pr merged commit 98520eb into 1187_decorate_output@main Nov 29, 2024
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m7pr deleted the tm_g_pp_patient_timeline@1187_decorate_output@main branch November 29, 2024 10:01

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introduce decorators to `tm_g_pp_patient_timeline` #1270

introduce decorators to `tm_g_pp_patient_timeline` #1270

llrs-roche commented Nov 28, 2024 •

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m7pr commented Nov 29, 2024

llrs-roche commented Nov 29, 2024

introduce decorators to tm_g_pp_patient_timeline #1270

introduce decorators to tm_g_pp_patient_timeline #1270

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m7pr commented Nov 29, 2024

llrs-roche commented Nov 29, 2024

introduce decorators to `tm_g_pp_patient_timeline` #1270

introduce decorators to `tm_g_pp_patient_timeline` #1270

llrs-roche commented Nov 28, 2024 •

edited

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