fix vline_vars display

[gogonzo]

closes #230

installation code

remotes::install_github(
  "insightsengineering/goshawk", 
  ref = "230_display_vline@main"
)

Example graph

pkgload::load_all("goshawk")
library(stringr)
library(tidyr)

# 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)

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(
    ANRHI = case_when(
      PARAMCD == "ALT" ~ 60,
      PARAMCD == "CRP" ~ 11,
      PARAMCD == "IGA" ~ 80,
      TRUE ~ NA_real_
    ),
    ANRLO = case_when(
      PARAMCD == "ALT" ~ 20,
      PARAMCD == "CRP" ~ 7,
      PARAMCD == "IGA" ~ 40,
      TRUE ~ NA_real_
    )
  ) %>%
  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[["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, flag_var = "LOQFL")
ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")

# given the 2 param and 2 analysis vars we need to transform the data
plot_data_t1 <- ADLB %>%
  gather(
    ANLVARS, ANLVALS, PARAM, LBSTRESC, BASE2, BASE, AVAL, BASE, LOQFL,
    ANRHI, ANRLO, ULOQN, LLOQN
  ) %>%
  mutate(ANL.PARAM = ifelse(ANLVARS %in% c("PARAM", "LBSTRESC", "LOQFL"),
    paste0(ANLVARS, "_", PARAMCD),
    paste0(ANLVARS, ".", PARAMCD)
  )) %>%
  select(USUBJID, ARM, ARMCD, AVISITN, AVISITCD, ANL.PARAM, ANLVALS) %>%
  spread(ANL.PARAM, ANLVALS)

# the transformed analysis value variables are character and need to be converted to numeric for
# ggplot
# remove records where either of the analysis variables are NA since they will not appear on the
# plot and will ensure that LOQFL = NA level is removed
plot_data_t2 <- plot_data_t1 %>%
  filter(!is.na(BASE.CRP) & !is.na(AVAL.ALT)) %>%
  mutate_at(vars(contains(".")), as.numeric) %>%
  mutate(
    LOQFL_COMB = ifelse(LOQFL_CRP == "Y" | LOQFL_ALT == "Y", "Y", "N")
  )


g_correlationplot(
  label = "Correlation Plot",
  data = plot_data_t2,
  param_var = "PARAMCD",
  xaxis_param = c("CRP"),
  xaxis_var = "AVAL",
  xvar = "AVAL.CRP",
  yaxis_param = c("ALT"),
  yaxis_var = "BASE",
  yvar = "BASE.ALT",
  trt_group = "ARM",
  visit = "AVISITCD",
  visit_facet = TRUE,
  loq_legend = TRUE,
  unit = "AVALU",
  title_text = "Correlation of ALT to CRP",
  xaxis_lab = "CRP",
  yaxis_lab = "ALT",
  color_manual = color_manual,
  shape_manual = shape_manual,
  facet_ncol = 4,
  facet = FALSE,
  facet_var = "ARM",
  reg_line = FALSE,
  vline_vars = c("ANRHI.CRP", "ANRLO.CRP", "ULOQN.CRP", "LLOQN.CRP"),
  vline_vars_colors = c("yellow", "orange", "brown", "gold"),
  vline_vars_labels = c("ANRHI CRP Label", "ANRLO CRP Label", "ULOQN CRP Label", "LLOQN CRP Label"),
  rotate_xlab = FALSE,
  font_size = 14,
  dot_size = 2,
  reg_text_size = 3
)

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: 2557bf5

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[npaszty]

the change looks very small.
not sure how to test this without establishing some infrastructure for testing like what we used to do: docker, staged dependencies etc. which I don't have time to do. or is there an easy way to test this now?

[gogonzo]

the change looks very small.
not sure how to test this without establishing some infrastructure for testing like what we used to do: docker, staged dependencies etc. which I don't have time to do. or is there an easy way to test this now?

Some way to install this is to:

• clone repo on your instance (ocean),
• checkout branch,
• install from local,
• then run the app

Or you can investigate example goshawk examples and confirm that issue on @main is addressed here.

Alternatively, we can review this within a team, merge it, deploy main to r-univers and then ask you to upgrade package from r-universe.

[npaszty]

@gogonzo

thanks for the explanations. I like the last one "Alternatively, we can review this within a team, merge it, deploy main to r-univers and then ask you to upgrade package from r-universe." 😄

[donyunardi]

@kartikeyakirar @gogonzo

Internally, we have Non-Validated-Dev that pulls from main branch. If @npaszty can't install this from the branch, then we can merge the PR and have Nick install this from Non-Validated-Dev/latest.

This way, we don't need to do any release.

[github-actions]

CLA Assistant Lite bot ✅ All contributors have signed the CLA

[cicdguy]

I have read the CLA Document and I hereby sign the CLA

[kartikeyakirar]

LGTM: tested with code

[kartikeyakirar]

@npaszty bugs are fixed and it is available in r-universe now.

[npaszty]

@kartikeyakirar

the horizontal/vertical and LLOQN/ULOQN functionality seems to be working well now. thanks!