289 xaxis lab for Line Plot & Spaghetti Plot

[m7pr]

Fixes #289 Test along with goshawk PR insightsengineering/goshawk#250

tm_g_gh_lineplot example

pkgload::load_all("../goshawk")
pkgload::load_all(".")
# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(stringr)
  library(nestcolor)
  
  # 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_lineplot(
      label = "Line Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      shape_choices = c("SEX", "RACE"),
      xaxis_var = choices_selected("AVISITCD", "AVISITCD"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      hline_arb = c(20.5, 19.5),
      hline_arb_color = c("red", "green"),
      hline_arb_label = c("A", "B")
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

tm_g_gh_spaghettiplot example

pkgload::load_all("../goshawk")
pkgload::load_all(".")
# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(stringr)
  
  # use non-exported function from goshawk
  h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
  
  # original ARM value = dose value
  arm_mapping <- list(
    "A: Drug X" = "150mg QD",
    "B: Placebo" = "Placebo",
    "C: Combination" = "Combination"
  )
  set.seed(1)
  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),
      ANRLO = 30,
      ANRHI = 75
    ) %>%
    rowwise() %>%
    group_by(PARAMCD) %>%
    mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
                             paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
    )) %>%
    mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
                             paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
    )) %>%
    ungroup()
  attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
  attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
  attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
  attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
  
  # add LLOQ and ULOQ variables
  ALB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
  ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")
})

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

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_spaghettiplot(
      label = "Spaghetti Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      idvar = "USUBJID",
      xaxis_var = choices_selected(c("Analysis Visit Code" = "AVISITCD"), "AVISITCD"),
      yaxis_var = choices_selected(c("AVAL", "CHG", "PCHG"), "AVAL"),
      filter_var = choices_selected(
        c("None" = "NONE", "Screening" = "BASE2", "Baseline" = "BASE"),
        "NONE"
      ),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_comb = "#39ff14",
      man_color = c(
        "Combination" = "#000000",
        "Placebo" = "#fce300",
        "150mg QD" = "#5a2f5f"
      ),
      hline_arb = c(60, 50),
      hline_arb_color = c("grey", "red"),
      hline_arb_label = c("default A", "default B"),
      hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
      hline_vars_colors = c("pink", "brown", "purple", "black"),
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Setting xlab for lineplot and spaghettiplot to Analysis Visit.

It is possible to change the label interactively with the new UI in Plot Settings

[github-actions]

Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  ---------
R/tm_g_gh_boxplot.R                        348     348  0.00%    175-591
R/tm_g_gh_correlationplot.R                555     555  0.00%    227-891
R/tm_g_gh_density_distribution_plot.R      273     273  0.00%    135-460
R/tm_g_gh_lineplot.R                       565     565  0.00%    163-825
R/tm_g_gh_scatterplot.R                    245     245  0.00%    144-442
R/tm_g_gh_spaghettiplot.R                  319     319  0.00%    196-601
R/toggleable_slider.R                      158     158  0.00%    73-248
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                          66      66  0.00%    2-98
R/utils.R                                   49      49  0.00%    12-112
R/zzz.R                                      2       2  0.00%    2-3
TOTAL                                     2933    2933  0.00%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/tm_g_gh_lineplot.R            +4      +4  +100.00%
R/tm_g_gh_spaghettiplot.R       +4      +4  +100.00%
TOTAL                           +8      +8  +100.00%

Results for commit: 84d111b

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[donyunardi]

We need to resolve this first:
insightsengineering/goshawk#250

[m7pr]

Closing in favour of insightsengineering/goshawk#259