[Bug]: How does one change the x-axis label for plots using tm_g_ipp?

[krissy-bios]

What happened?

How do I change the x-axis label for the timepoint variable? One feature of teal that we love is the ability to select the x-axis variable from a drop down menu since we have varying definitions of timepoint in our study. However, there doesn't appear to be a way to change the x-axis label associated with this variable. This is a bug, or an oversight, because it creates incorrect plots if the label "Visit" is the appropriate selection. Nor does it allow me to add the units of the visit variable to the axis label, which is also important. In addition, it is feasible to also create plots across the age of the individual, not simply the time. Retaining the x-axis simply as a timepoint variable prevents one from utilizing the graphing future to its fullest extent. Please let me know if I am missing this in the documentation or if this is a change that may be made in the program itself. Thank you!

sessionInfo()

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[lcd2yyz]

Thanks @krissy-bios for reporting and sharing your broader use case, we'll look into it.

[edelarua]

Hi @krissy-bios,

Although this does not fix some of the displayed text hard-coded into the options panel for the module, please note that for now you can customize the x-axis text via the ggplot2_args argument as follows (using the module example code as an example):

library(nestcolor)

ADSL <- tmc_ex_adsl %>%
  dplyr::slice(1:20) %>%
  df_explicit_na()
ADLB <- tmc_ex_adlb %>%
  dplyr::filter(USUBJID %in% ADSL$USUBJID) %>%
  df_explicit_na() %>%
  dplyr::filter(AVISIT != "SCREENING")

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADLB = ADLB,
    code = "
      ADSL <- tmc_ex_adsl %>% dplyr::slice(1:20) %>% df_explicit_na()
      ADLB <- tmc_ex_adlb %>% dplyr::filter(USUBJID %in% ADSL$USUBJID) %>%
        df_explicit_na() %>% dplyr::filter(AVISIT != \"SCREENING\")
    "
  ),
  modules = modules(
    tm_g_ipp(
      label = "Individual Patient Plot",
      dataname = "ADLB",
      arm_var = choices_selected(
        value_choices(ADLB, "ARMCD"),
        "ARM A"
      ),
      paramcd = choices_selected(
        value_choices(ADLB, "PARAMCD"),
        "ALT"
      ),
      aval_var = choices_selected(
        variable_choices(ADLB, c("AVAL", "CHG")),
        "AVAL"
      ),
      avalu_var = choices_selected(
        variable_choices(ADLB, c("AVALU")),
        "AVALU",
        fixed = TRUE
      ),
      id_var = choices_selected(
        variable_choices(ADLB, c("USUBJID")),
        "USUBJID",
        fixed = TRUE
      ),
      visit_var = choices_selected(
        variable_choices(ADLB, c("AVISIT")),
        "AVISIT"
      ),
      base_var = choices_selected(
        variable_choices(ADLB, c("BASE")),
        "BASE",
        fixed = TRUE
      ),
      add_baseline_hline = FALSE,
      separate_by_obs = FALSE,
      ggplot2_args = teal.widgets::ggplot2_args(
        labs = list(x = "Custom x-axis text")
      )
    )
  )
)
if (interactive()) {
  shinyApp(ui = app$ui, server = app$server)
}

Let me know if this helps!

[nicolekjones]

Hi, chiming in here (I work along side Krissy :D) :

Would this solve this issue? In the example we're using three different visit variables. So would need to dynamically update the x-axis label based on what variable is selected as the visit variable. Please see example below on how how we implement tm_g_ipp:

 tm_g_ipp(
    label = "Lab Plots",
    dataname = "LabFindings",
    arm_var = choices_selected(
      value_choices(adlb, "COHORT"),
      "P1"
    ),
    paramcd = choices_selected(
      value_choices(adlb, c("PARAM"), var_label = c("PARAM"))
    ),
    aval_var = choices_selected(
      variable_choices(adlb, c("AVAL", "CHG", "PCHG")),
      "CHG"
    ),
    avalu_var = choices_selected(
      variable_choices(adlb, c("AVALU")),
      "AVALU",
      fixed = TRUE
    ),
    id_var = choices_selected(
      variable_choices(adlb, c("SUBJID")),
      "SUBJID",
      fixed = TRUE
    ),
    visit_var = choices_selected(
      variable_choices(adlb, c("AVISIT", "ADY1", "ADY2","AGEASS")),
      "AVISIT"
    ),
    base_var = choices_selected(
      variable_choices(adlb, c("BASE")),
      "BASE",
      fixed = TRUE
    ),
    add_baseline_hline = FALSE,
    separate_by_obs = FALSE,
    plot_height = c(400L, 400L, 5000L)
  )