add loqfl legend

[gogonzo]

Closes #231

Including shape parameter based on loq_flag_var value.

Install goshawk from the branch

installation code

remotes::install_github(
  "insightsengineering/goshawk", 
  ref = "231_shape_on_loqfl@main"
)

goshawk examples

pkgload::load_all("goshawk")
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 <- 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, "LOQFL")
ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")

g_spaghettiplot(
  data = ADLB,
  subj_id = "USUBJID",
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  time = "AVISITCD",
  color_manual = color_manual,
  color_comb = "#39ff14",
  alpha = .02,
  xtick = c("BL", "W 1", "W 4"),
  xlabel = c("Baseline", "Week 1", "Week 4"),
  rotate_xlab = FALSE,
  group_stats = "median",
  hline_vars = c("ANRHI", "ANRLO"),
  hline_vars_colors = c("pink", "brown")
)

g_spaghettiplot(
  data = ADLB,
  subj_id = "USUBJID",
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  time = "AVISITCD",
  color_manual = color_manual,
  color_comb = "#39ff14",
  alpha = .02,
  xtick = c("BL", "W 1", "W 4"),
  xlabel = c("Baseline", "Week 1", "Week 4"),
  rotate_xlab = FALSE,
  group_stats = "median",
  hline_arb = 1.3,
  hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
  hline_vars_colors = c("pink", "brown", "purple", "gray")
)

g_spaghettiplot(
  data = ADLB,
  subj_id = "USUBJID",
  biomarker_var = "PARAMCD",
  biomarker = "CRP",
  value_var = "AVAL",
  trt_group = "ARM",
  time = "AVISITCDN",
  color_manual = color_manual,
  color_comb = "#39ff14",
  alpha = .02,
  xtick = c(0, 1, 4),
  xlabel = c("Baseline", "Week 1", "Week 4"),
  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")
)

# removing missing levels from the plot with facet_scales

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")
)

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")
)

main	this

[github-actions]

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  ---------
R/g_boxplot.R                        116     116  0.00%    147-310
R/g_correlationplot.R                135     135  0.00%    251-419
R/g_density_distribution_plot.R       86      86  0.00%    125-236
R/g_lineplot.R                       275     275  0.00%    262-606
R/g_scatterplot.R                    130     130  0.00%    142-310
R/g_spaghettiplot.R                  102     102  0.00%    243-376
R/geom_axes_line.R                   167     167  0.00%    46-358
R/t_summarytable.R                   102     102  0.00%    87-224
R/utils.R                             70      70  0.00%    17-137
TOTAL                               1183    1183  0.00%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 995a50f

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[npaszty]

@gogonzo

similar comment to that which I left in PR #233

[kartikeyakirar]

LGTM: test with sample code.

[npaszty]

@kartikeyakirar

first, thanks for adding the LoQ legend to spaghetti plot but would it be possible to re-open this issue?

The current size of the symbols in the legend and on the lines in the spaguetti plot are too small to interpret. can you look at the other functions to see how the legend symbol size and the plot symbol size is being set and match that. thanks!

[kartikeyakirar]

@npaszty Let me open a separate issue instead of reopening this one. I will link this issue for reference.

issue: #241

[kartikeyakirar]

@npaszty The point size issue has been resolved and the update has been released to R-universe. The default point size is set to 3, but you can customize it by setting dot_size parameter in the function.