Correlation

[npaszty]

when adding LLOQ vertical line, the legend doesn't update. same with SRC.
when adding LLOQ horizontal line, the legend updates and the vertical line also appears now.
see app.R here:
/home/bceuser/npaszty/lupus_data_mart/sandbox

[nikolas-burkoff]

Reprex below @gogonzo

Separately @npaszty https://github.com/insightsengineering/coredev-tasks/issues/285

library(scda)
library(teal.goshawk)

# 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")
# assign LOQ flag symbols: circles for "N" and triangles for "Y", squares for "NA"
shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)

ADSL <- synthetic_cdisc_data("latest")$adsl

set.seed(1)
ADLB <- synthetic_cdisc_data("latest")$adlb
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
  dplyr::mutate(AVISITCD = dplyr::case_when(
    AVISIT == "SCREENING" ~ "SCR",
    AVISIT == "BASELINE" ~ "BL",
    grepl("WEEK", AVISIT) ~
      paste(
        "W",
        trimws(
          substr(
            AVISIT,
            start = 6,
            stop = stringr::str_locate(AVISIT, "DAY") - 1
          )
        )
      ),
    TRUE ~ NA_character_
  )) %>%
  dplyr::mutate(AVISITCDN = dplyr::case_when(
    AVISITCD == "SCR" ~ -2,
    AVISITCD == "BL" ~ 0,
    grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
    TRUE ~ NA_real_
  )) %>%
  # use ARMCD values to order treatment in visualization legend
  dplyr::mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
                                ifelse(grepl("B", ARMCD), 2,
                                       ifelse(grepl("A", ARMCD), 3, NA)
                                )
  )) %>%
  dplyr::mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
  dplyr::mutate(ARM = factor(ARM) %>%
                  reorder(TRTORD)) %>%
  dplyr::mutate(
    ANRHI = dplyr::case_when(
      PARAMCD == "ALT" ~ 60,
      PARAMCD == "CRP" ~ 70,
      PARAMCD == "IGA" ~ 80,
      TRUE ~ NA_real_
    ),
    ANRLO = dplyr::case_when(
      PARAMCD == "ALT" ~ 20,
      PARAMCD == "CRP" ~ 30,
      PARAMCD == "IGA" ~ 40,
      TRUE ~ NA_real_
    )
  ) %>%
  dplyr::rowwise() %>%
  dplyr::group_by(PARAMCD) %>%
  dplyr::mutate(LBSTRESC = ifelse(
    USUBJID %in% sample(USUBJID, 1, replace = TRUE),
    paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
  )) %>%
  dplyr::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[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"

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

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
    cdisc_dataset(
      "ADLB",
      ADLB,
      code = "set.seed(1)
              ADLB <- synthetic_cdisc_data('latest')$adlb
              var_labels <- lapply(ADLB, function(x) attributes(x)$label)
              ADLB <- ADLB %>%
                dplyr::mutate(AVISITCD = dplyr::case_when(
                  AVISIT == 'SCREENING' ~ 'SCR',
                  AVISIT == 'BASELINE' ~ 'BL',
                  grepl('WEEK', AVISIT) ~
                    paste(
                      'W',
                      trimws(
                        substr(
                          AVISIT,
                          start = 6,
                          stop = stringr::str_locate(AVISIT, 'DAY') - 1
                        )
                      )
                    ),
                  TRUE ~ NA_character_)) %>%
                dplyr::mutate(AVISITCDN = dplyr::case_when(
                  AVISITCD == 'SCR' ~ -2,
                  AVISITCD == 'BL' ~ 0,
                  grepl('W', AVISITCD) ~ as.numeric(gsub('[^0-9]*', '', AVISITCD)),
                  TRUE ~ NA_real_)) %>%
                # use ARMCD values to order treatment in visualization legend
                dplyr::mutate(TRTORD = ifelse(grepl('C', ARMCD), 1,
                                       ifelse(grepl('B', ARMCD), 2,
                                              ifelse(grepl('A', ARMCD), 3, NA)))) %>%
                dplyr::mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
                dplyr::mutate(ARM = factor(ARM) %>%
                         reorder(TRTORD)) %>%
                dplyr::mutate(
                  ANRHI = dplyr::case_when(
                    PARAMCD == 'ALT' ~ 60,
                    PARAMCD == 'CRP' ~ 70,
                    PARAMCD == 'IGA' ~ 80,
                    TRUE ~ NA_real_
                  ),
                  ANRLO = dplyr::case_when(
                    PARAMCD == 'ALT' ~ 20,
                    PARAMCD == 'CRP' ~ 30,
                    PARAMCD == 'IGA' ~ 40,
                    TRUE ~ NA_real_
                  )) %>%
                dplyr::rowwise() %>%
                dplyr::group_by(PARAMCD) %>%
                dplyr::mutate(LBSTRESC = ifelse(
                  USUBJID %in% sample(USUBJID, 1, replace = TRUE),
                  paste('<', round(runif(1, min = 25, max = 30))), LBSTRESC)) %>%
                dplyr::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[['ANRHI']], 'label') <- 'Analysis Normal Range Upper Limit'
              attr(ADLB[['ANRLO']], 'label') <- 'Analysis Normal Range Lower Limit'
              # add LLOQ and ULOQ variables
              ADLB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
          ADLB <- left_join(ADLB, ADLB_LOQS, by = 'PARAM')",
      vars = list(arm_mapping = arm_mapping)
    ),
    check = TRUE
  ),
  modules = modules(
    tm_g_gh_correlationplot(
      label = "Correlation Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      xaxis_param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
      yaxis_param = choices_selected(c("ALT", "CRP", "IGA"), "CRP"),
      xaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "BASE"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      color_manual = c(
        "Drug X 100mg" = "#000000",
        "Placebo" = "#3498DB",
        "Combination 100mg" = "#E74C3C"
      ),
      shape_manual = c("N" = 1, "Y" = 2, "NA" = 0),
      plot_height = c(500, 200, 2000),
      facet_ncol = 2,
      visit_facet = TRUE,
      reg_line = FALSE,
      loq_legend = TRUE,
      font_size = c(12, 8, 20),
      dot_size = c(1, 1, 12),
      reg_text_size = c(3, 3, 10),
      hline_vars = c("ULOQN", "LLOQN"),
      hline_vars_colors = c("purple", "gray"),
      hline_vars_labels =  c("Upper Limit of Quantitation", "Lower Limit of Quantitation"),
      vline_vars = c("ULOQN", "LLOQN"),
      vline_vars_colors = c("brown", "gold"),
      vline_vars_labels =  c("Upper Limit of Quantitation", "Lower Limit of Quantitation")
    )
  )
)

shinyApp(app$ui, app$server)

[nikolas-burkoff]

After discussions we'll keep this in the release sprint but I'll move my additional comments above into a new goshawk issue for the backlog

[kpagacz]

@nikolas-burkoff @gogonzo The release sprint ended, and this issue was left out. I guess some of its substance got moved to the new issue. What shall we do with this one then?

Is this being actively worked on?

[gogonzo]

@kpagacz thanks, you are right I'm closing this one if favour of these two

#139

https://github.com/insightsengineering/coredev-tasks/issues/285