Calculate density ranges based on treatment name and based on AVICITCD for density plot

[m7pr]

Fixes insightsengineering/goshawk#192

For proper density calculations, you need to calculate ranges within groups inside the plot. Groups are created based on treatment variable and based on AVICITCD plot. So the max ranges need to be calculated in each group, and the max needs to be extracted.

Set filters to: ADSL -> SEX -> Male, ADSL -> AGE -> 31.41, 35

How it looked before

How it looks now

Example code

Example from `?tm_g_gh_density_distribution_plot`

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

data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(stringr)
  
  # original ARM value = dose value
  arm_mapping <- list(
    "A: Drug X" = "150mg QD",
    "B: Placebo" = "Placebo",
    "C: Combination" = "Combination"
  )
  ADSL <- rADSL
  ADLB <- rADLB
  var_labels <- lapply(ADLB, function(x) attributes(x)$label)
  ADLB <- ADLB %>%
    mutate(
      AVISITCD = case_when(
        AVISIT == "SCREENING" ~ "SCR",
        AVISIT == "BASELINE" ~ "BL",
        grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
        TRUE ~ as.character(NA)
      ),
      AVISITCDN = case_when(
        AVISITCD == "SCR" ~ -2,
        AVISITCD == "BL" ~ 0,
        grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
        TRUE ~ as.numeric(NA)
      ),
      AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
      TRTORD = case_when(
        ARMCD == "ARM C" ~ 1,
        ARMCD == "ARM B" ~ 2,
        ARMCD == "ARM A" ~ 3
      ),
      ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
      ARM = factor(ARM) %>% reorder(TRTORD),
      ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
      ACTARM = factor(ACTARM) %>% reorder(TRTORD)
    )
  
  attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
  attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
})

datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_density_distribution_plot(
      label = "Density Distribution Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "150mg QD" = "#000000",
        "Placebo" = "#3498DB",
        "Combination" = "#E74C3C"
      ),
      color_comb = "#39ff14",
      comb_line = TRUE,
      plot_height = c(500, 200, 2000),
      font_size = c(12, 8, 20),
      line_size = c(1, .25, 3),
      hline_arb = c(.02, .05),
      hline_arb_color = c("red", "black"),
      hline_arb_label = c("Horizontal Line A", "Horizontal Line B")
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

[github-actions]

Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  ---------
R/tm_g_gh_boxplot.R                        352     352  0.00%    175-594
R/tm_g_gh_correlationplot.R                555     555  0.00%    227-891
R/tm_g_gh_density_distribution_plot.R      279     279  0.00%    135-464
R/tm_g_gh_lineplot.R                       565     565  0.00%    161-820
R/tm_g_gh_scatterplot.R                    245     245  0.00%    144-441
R/tm_g_gh_spaghettiplot.R                  315     315  0.00%    194-590
R/toggleable_slider.R                      154     154  0.00%    72-243
R/utils-arbitrary_lines.r                  125     125  0.00%    19-176
R/utils-data_constraints.r                 190     190  0.00%    2-257
R/utils-keep_range_slider_updated.r         29      29  0.00%    9-45
R/utils-maptrt.r                             9       9  0.00%    24-36
R/utils-templ_ui.r                          48      48  0.00%    2-73
R/utils.R                                   49      49  0.00%    12-112
R/zzz.R                                      2       2  0.00%    2-3
TOTAL                                     2917    2917  0.00%

Diff against main

Filename                                 Stmts    Miss  Cover
-------------------------------------  -------  ------  --------
R/tm_g_gh_density_distribution_plot.R       +1      +1  +100.00%
R/utils-keep_range_slider_updated.r         +6      +6  +100.00%
TOTAL                                       +7      +7  +100.00%

Results for commit: ae19dbb

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[donyunardi]

Looks good!

There several linting issues in CI/CD but all seems small.
Feel free to fix and merge once addressed.