Custom rendering to provide manual ticks when there is <10 ticks #319

vedhav · 2024-10-10T12:09:23Z

Closes #133

Example app to test:

devtools::load_all()
# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
  library(dplyr)
  library(nestcolor)
  library(stringr)

  # use non-exported function from goshawk
  h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")

  # original ARM value = dose value
  arm_mapping <- list(
    "A: Drug X" = "150mg QD",
    "B: Placebo" = "Placebo",
    "C: Combination" = "Combination"
  )
  set.seed(1)
  ADSL <- rADSL
  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", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
        TRUE ~ as.character(NA)
      ),
      AVISITCDN = case_when(
        AVISITCD == "SCR" ~ -2,
        AVISITCD == "BL" ~ 0,
        grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
        TRUE ~ as.numeric(NA)
      ),
      AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
      TRTORD = case_when(
        ARMCD == "ARM C" ~ 1,
        ARMCD == "ARM B" ~ 2,
        ARMCD == "ARM A" ~ 3
      ),
      ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
      ARM = factor(ARM) %>% reorder(TRTORD),
      ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
      ACTARM = factor(ACTARM) %>% reorder(TRTORD),
      ANRLO = 50,
      ANRHI = 75
    ) %>%
    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[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
  attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
  attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"

  # add LLOQ and ULOQ variables
  ALB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
  ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")
})

datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames


join_keys(data) <- default_cdisc_join_keys[datanames]

app <- init(
  data = data,
  modules = modules(
    tm_g_gh_boxplot(
      label = "Box Plot",
      dataname = "ADLB",
      param_var = "PARAMCD",
      param = choices_selected(c("ALT", "CRP", "IGA"), "CRP"),
      yaxis_var = choices_selected(c("AVAL", "BASE", "CHG"), "AVAL"),
      xaxis_var = choices_selected(c("ACTARM", "ARM", "AVISITCD", "STUDYID"), "ARM"),
      facet_var = choices_selected(c("ACTARM", "ARM", "AVISITCD", "SEX"), "AVISITCD"),
      trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
      loq_legend = TRUE,
      rotate_xlab = FALSE,
      hline_arb = c(60, 55),
      hline_arb_color = c("grey", "red"),
      hline_arb_label = c("default_hori_A", "default_hori_B"),
      hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
      hline_vars_colors = c("pink", "brown", "purple", "black"),
    )
  )
)

shinyApp(app$ui, app$server)

R/toggleable_slider.R

github-actions · 2024-10-10T12:14:26Z

Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  ---------------------------------------------------------
R/tm_g_gh_boxplot.R                        345      30  91.30%   365, 371, 510-511, 519-542, 544-545
R/tm_g_gh_correlationplot.R                566     566  0.00%    227-903
R/tm_g_gh_density_distribution_plot.R      272     272  0.00%    135-460
R/tm_g_gh_lineplot.R                       557     557  0.00%    161-812
R/tm_g_gh_scatterplot.R                    254     254  0.00%    144-452
R/tm_g_gh_spaghettiplot.R                  319     319  0.00%    194-596
R/toggleable_slider.R                      112       7  93.75%   140-146
R/utils-arbitrary_lines.r                  125      14  88.80%   63, 74-77, 81, 93-96, 110, 114, 121, 125
R/utils-data_constraints.r                 190      61  67.89%   39, 57, 111-124, 126-140, 154, 177, 183, 202-228, 243-252
R/utils-maptrt.r                             9       9  0.00%    24-36
R/utils-templ_ui.r                          66      17  74.24%   2-7, 40-43, 73-79
R/utils.R                                   49      40  18.37%   12-19, 26, 60-112
R/zzz.R                                      2       2  0.00%    2-3
TOTAL                                     2866    2148  25.05%

Diff against main

Filename                                 Stmts    Miss  Cover
-------------------------------------  -------  ------  --------
R/tm_g_gh_boxplot.R                         -4    -319  +91.30%
R/tm_g_gh_correlationplot.R                +10     +10  +100.00%
R/tm_g_gh_density_distribution_plot.R       -2      -2  +100.00%
R/tm_g_gh_lineplot.R                        -5      -5  +100.00%
R/tm_g_gh_scatterplot.R                     +8      +8  +100.00%
R/tm_g_gh_spaghettiplot.R                   +3      +3  +100.00%
R/toggleable_slider.R                      -46    -151  +93.75%
R/utils-arbitrary_lines.r                    0    -111  +88.80%
R/utils-data_constraints.r                   0    -129  +67.89%
R/utils-templ_ui.r                           0     -49  +74.24%
R/utils.R                                    0      -9  +18.37%
TOTAL                                      -36    -754  +25.05%

Results for commit: 5990855

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

m7pr · 2024-10-10T12:58:10Z

@vedhav The slider does not affect the output of the plot : ( plot Y-Axis should be reduced to the limits set in the slider

vedhav · 2024-10-10T13:00:18Z

Ah, I can see why this could happen. Let me check.

vedhav · 2024-10-10T13:28:21Z

@m7pr that bug is fixed. I stumbled upon another bug, When some inputs change (in the top widgets, like the Select an X-Axis Biomarker), the slider range is set again to new limits, currently this is not happening. I'm working on this case.

donyunardi

Thanks for the work, @vedhav

I have couple findings:

The plot and slider got reset to original value after clicking the Toggle button a few times:

Screen.Recording.2024-10-11.at.8.27.54.AM.mov

On 0:18 to 0:20, you can see the plot changes before I click the Toggle button.
This doesn't happen in main branch.

When I changed the X-Axis Biomarker to ALT, the numbers in ticks are overlapping toward the end of the slider:

…ivity issue

vedhav · 2024-10-16T06:59:31Z

@donyunardi Please have a look now. There was another reactivity issue, its getting harder and harder to maintain this, we might have to invest some time in implementing this as a component in teal.widgets.
The tick overlap is also fixed now.

m7pr · 2024-10-16T07:09:37Z

guidelines for the review https://github.com/insightsengineering/coredev-tasks/issues/590

R/toggleable_slider.R

Closes #321 Changes: 1. The `toggle_slider_ui` and `toggle_slider_server` can only be used to create dichotomous slider now. There was no instance of single value slider created. So, there is no need to create it and increase the complexity. 2. Removal of the `keep_range_slider_updated` in favor of `keep_slider_state_updated` to keep the states updated based on other widget inputs. 3. Updated the modules that uses this widget. Note that the `tm_g_gh_lineplot` does not use the `keep_slider_state_updated` and directly updates the state reactiveValues. Check all the modules that use the `toggle_slider` module: - [ ] `tm_g_gh_boxplot` - [ ] `tm_g_gh_correlationplot` - [ ] `tm_g_gh_density_distribution_plot` - [ ] `tm_g_gh_lineplot` - [ ] `tm_g_gh_spaghettiplot` - [ ] `tm_g_gh_scatterplot `(deprecate in favor of `tm_g_gh_correlationplot`) --------- Co-authored-by: go_gonzo <[email protected]>

changes have been made

github-actions · 2024-10-28T14:19:18Z

Unit Tests Summary

1 files 1 suites 56s ⏱️
6 tests 6 ✅ 0 💤 0 ❌
12 runs 12 ✅ 0 💤 0 ❌

Results for commit 0be5c7f.

♻️ This comment has been updated with latest results.

gogonzo

Works as expected. Merge once R CMD check is fixed. Great job 💪

feat: custom rendering to provide manual ticks when there is <10 ticks

d8e3548

vedhav added bug Something isn't working core labels Oct 10, 2024

vedhav requested a review from m7pr October 10, 2024 12:09

vedhav commented Oct 10, 2024

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vedhav added 2 commits October 10, 2024 17:54

chore: update docs

6468f33

chore: simplify slider states logic

754ac20

Merge branch 'main' into 133-improve-slider-ticks@main

f66482e

fix: make the slider work + fix recursive auto update

28e08af

vedhav added 2 commits October 11, 2024 17:57

fix: re-render the slider when min and max state range changes

51eb85b

fix: trigger update using the keep_range_slider_updated logic

046b119

vedhav requested a review from donyunardi October 11, 2024 13:29

Merge branch 'main' into 133-improve-slider-ticks@main

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vedhav enabled auto-merge (squash) October 11, 2024 15:24

donyunardi disabled auto-merge October 11, 2024 15:30

donyunardi previously requested changes Oct 11, 2024

View reviewed changes

fix: reset of slider state on toggle

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vedhav requested a review from donyunardi October 15, 2024 15:45

fix: manually hide the last before tick when it is closer + fix react…

4a25b28

…ivity issue

gogonzo requested changes Oct 16, 2024

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vedhav added 3 commits October 16, 2024 16:45

chore: remove redundant code

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chore: remove unwanted condition

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chore: add package prefix

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gogonzo reviewed Oct 16, 2024

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chore: simplify

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gogonzo reviewed Oct 16, 2024

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gogonzo self-assigned this Oct 17, 2024

vedhav mentioned this pull request Oct 18, 2024

Refactor the toggle slider in the package based on the comment #321

Open

vedhav and others added 2 commits October 28, 2024 19:36

Merge branch 'main' into 133-improve-slider-ticks@main

d990877

vedhav requested a review from gogonzo October 28, 2024 14:09

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

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vedhav enabled auto-merge (squash) October 28, 2024 14:13

gogonzo approved these changes Oct 28, 2024

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chore: add test dependencies to suggests

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vedhav merged commit 7907046 into main Oct 28, 2024
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vedhav deleted the 133-improve-slider-ticks@main branch October 28, 2024 15:50

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Custom rendering to provide manual ticks when there is <10 ticks #319

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Custom rendering to provide manual ticks when there is <10 ticks #319

Custom rendering to provide manual ticks when there is <10 ticks #319

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