219 scales parameter for facet_wrap in g_spaghettiplot

[m7pr]

Fix for insightsengineering/teal.goshawk#219 and continued here insightsengineering/teal.goshawk#227

Data

library(stringr)

# original ARM value = dose value
arm_mapping <- list(
  "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination"
)
color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")

ADLB <- goshawk::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",
        trimws(
          substr(
            AVISIT,
            start = 6,
            stop = str_locate(AVISIT, "DAY") - 1
          )
        )
      ),
    TRUE ~ NA_character_
  )) %>%
  mutate(AVISITCDN = case_when(
    AVISITCD == "SCR" ~ -2,
    AVISITCD == "BL" ~ 0,
    grepl("W", AVISITCD) ~ as.numeric(gsub("\\D+", "", AVISITCD)),
    TRUE ~ NA_real_
  )) %>%
  # use ARMCD values to order treatment in visualization legend
  mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
    ifelse(grepl("B", ARMCD), 2,
      ifelse(grepl("A", ARMCD), 3, NA)
    )
  )) %>%
  mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
  mutate(ARM = factor(ARM) %>%
    reorder(TRTORD)) %>%
  mutate(ANRLO = .5, ANRHI = 1) %>%
  rowwise() %>%
  group_by(PARAMCD) %>%
  mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
    paste("<", round(runif(1, min = .5, max = .7))), LBSTRESC
  )) %>%
  mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
    paste(">", round(runif(1, min = .9, max = 1.2))), LBSTRESC
  )) %>%
  ungroup()
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"

# add LLOQ and ULOQ variables
ADLB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")

Show all scales - facet_scales = 'fixed'

g_spaghettiplot(
  data = ADLB,
  subj_id = "USUBJID",
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  time = "RACE",
  color_manual = color_manual,
  color_comb = "#39ff14",
  alpha = .02,
  facet_scales = "fixed",
  rotate_xlab = FALSE,
  group_stats = "median",
  hline_arb = c(.5, .7, 1),
  hline_arb_color = c("blue", "red", "green"),
  hline_arb_label = c("Arb_Hori_line_A", "Arb_Hori_line_B", "Arb_Hori_line_C"),
  hline_vars = c("ANRHI", "ANRLO")
)

Free scales for x - facet_scales = 'free_x'

g_spaghettiplot(
  data = ADLB,
  subj_id = "USUBJID",
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  time = "RACE",
  color_manual = color_manual,
  color_comb = "#39ff14",
  alpha = .02,
  facet_scales = "free_x",
  rotate_xlab = FALSE,
  group_stats = "median",
  hline_arb = c(.5, .7, 1),
  hline_arb_color = c("blue", "red", "green"),
  hline_arb_label = c("Arb_Hori_line_A", "Arb_Hori_line_B", "Arb_Hori_line_C"),
  hline_vars = c("ANRHI", "ANRLO")
)

[github-actions]

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  ---------
R/g_boxplot.R                        108     108  0.00%    148-303
R/g_correlationplot.R                129     129  0.00%    251-413
R/g_density_distribution_plot.R       86      86  0.00%    125-236
R/g_lineplot.R                       256     256  0.00%    261-586
R/g_scatterplot.R                    123     123  0.00%    142-303
R/g_spaghettiplot.R                  101     101  0.00%    242-375
R/geom_axes_line.R                   167     167  0.00%    48-370
R/t_summarytable.R                   102     102  0.00%    87-224
R/utils.R                             68      68  0.00%    18-134
TOTAL                               1140    1140  0.00%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  --------
R/g_spaghettiplot.R       +1      +1  +100.00%
TOTAL                     +1      +1  +100.00%

Results for commit: fcfa8e1

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results