From 4f90f9f26854fc64d516b41cd805150fc22a8a12 Mon Sep 17 00:00:00 2001
From: Marcin <133694481+m7pr@users.noreply.github.com>
Date: Thu, 10 Oct 2024 14:50:26 +0200
Subject: [PATCH] 249 remove analysis variable name plot title in spaghettiplot
 (#251)

Close #249

Before the change
<img width="605" alt="title_before"
src="https://github.com/user-attachments/assets/381412d0-a98d-4440-bdc4-3c1f51fec9aa">


After the change

<img width="606" alt="after"
src="https://github.com/user-attachments/assets/518649a6-1442-49ec-9aa2-711fa4ef9580">


Tested with below

```r
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")
)

```

---------

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
---
 R/g_spaghettiplot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/g_spaghettiplot.R b/R/g_spaghettiplot.R
index 69d254e3..9046d69a 100644
--- a/R/g_spaghettiplot.R
+++ b/R/g_spaghettiplot.R
@@ -279,7 +279,7 @@ g_spaghettiplot <- function(data,
     select(!!sym(biomarker_var_label)) %>%
     unique() %>%
     magrittr::extract2(1)
-  gtitle <- paste0(biomarker1, unit1, value_var, " Values by Treatment @ Visits")
+  gtitle <- paste0(biomarker1, unit1, " Values by Treatment @ Visits")
   gxlab <- if (is.null(attr(data[[time]], "label"))) time else attr(data[[time]], "label")
   gylab <- paste0(biomarker1, " ", value_var, " Values")