Initial commit

.Rbuildignore

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+.*Rproj
+^\.Rproj\.user$
+^LICENSE$
+^README\.Rmd$
+^README\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+.lintr
+inst/validation/results/.gitempty

.github/CODEOWNERS

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+*   @boehringer-ingelheim/davinci

.github/workflows/ci.yml

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+---
+name: Checks 🧩
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  run-shared-ci:
+    name: Shared
+    uses: boehringer-ingelheim/dv.templates/.github/workflows/shared_ci.yml@main

.github/workflows/mytest.yml

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+---
+name: Test and QC 🧪
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+concurrency:
+  group: test-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  TEMPLATE_REF: main
+  TEMPLATE_REPO: boehringer-ingelheim/dv.templates
+
+jobs:
+  test:
+    name: ${{ vars.CI_IMAGE }}
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ vars.CI_IMAGE }}    
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout project ⬇️
+        uses: actions/checkout@v4
+
+      - name: Checkout templates repo ⬇️  
+        uses: actions/checkout@v4
+        with:
+          ref: ${{env.TEMPLATE_REF}}
+          repository: ${{env.TEMPLATE_REPO}}
+          sparse-checkout: |
+            scripts/
+            inst/validation
+          path: templates
+
+      - name: Overwrite quality control scripts with dv.templates ones 🧹
+        shell: bash
+        run: |
+          TEMPLATE_DIR="templates/inst/validation"
+          REPO_DIR="inst/validation"
+
+          if test ! -d "${REPO_DIR}"; then
+            echo "### Quality Control documentation is not present"
+            echo "### Include quality control documentation or skip it by creating following file 'inst/validation/skip_qc'"
+            exit 1
+          fi
+
+          if test -f "${REPO_DIR}/skip_qc"; then
+            echo "skip_qc file found skipping qc documentation"
+            exit 0
+          fi
+          
+          # Conserve specs.R file
+          cp "${REPO_DIR}/specs.R" "${TEMPLATE_DIR}/specs.R"
+
+          set +e  # Disable immediate exit in conflicting parts on error for diff command
+          DIFF_OUTPUT=$(diff -qr "${TEMPLATE_DIR}" "${REPO_DIR}")
+          set -e  # Enable immediate exit on error after diff command
+
+          echo "# Quality control files" | tee -a "${GITHUB_STEP_SUMMARY}"
+          
+          if [ -n "${DIFF_OUTPUT}" ]; then
+            echo "Warning: The contents of the directories are different!" | tee -a "${GITHUB_STEP_SUMMARY}"
+            echo "Modified files:" | tee -a "${GITHUB_STEP_SUMMARY}"
+            echo "$DIFF_OUTPUT" | tee -a "${GITHUB_STEP_SUMMARY}"
+          else
+            echo "The directories are identical." | tee -a "${GITHUB_STEP_SUMMARY}"
+          fi
+
+          rm -rf "${REPO_DIR}"
+          mv "${TEMPLATE_DIR}" "${REPO_DIR}"
+
+      - name: Install package dependencies 📄
+        uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main     
+
+      - name: Test and QC2 🧪        
+        run: Rscript templates/scripts/test_qc_pkg.R
+
+      - name: Archive snap results ⬆️
+        uses: actions/upload-artifact@v4
+        with:
+          name: snap_results
+          path: tests/testthat/_snaps
+

.gitignore

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+.vscode
+.Rproj.user
+.Rhistory
+*.Rproj
+docs/

.lintr

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+linters: linters_with_defaults(
+  line_length_linter(120),
+  object_usage_linter = NULL,
+  indentation_linter = NULL,
+  trailing_whitespace_linter = NULL
+  )
+
+

DESCRIPTION

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+Package: dv.biomarker.general
+Type: Package
+Title: Biomarker Visualization Modules
+Version: 0.0.4-900
+Authors@R: c(
+        person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
+        person(given = "Luis", family = "Moris Fernandez", role = c("aut", "cre"), email = "[email protected]"),
+        person(given = "Miguel", family = "Lechon", role = c("aut"), email = "[email protected]")
+        )
+Description: not-EBAS Modules.
+License: Apache License (>= 2)
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Suggests: dv.manager (>= 1.0.9.129), jsonlite, rmarkdown, testthat (>=
+        3.0.0), shinytest2, devtools, vdiffr, rvest, stringr, knitr,
+        safetyData, png, rsvg, withr
+Config/testthat/edition: 3
+Config/testthat/parallel: false
+Imports: shiny (>= 1.7.1),dplyr (>= 1.0.7), broom (>= 0.7.9), ggplot2
+        (>= 3.3.5), DT (>= 0.19), purrr (>= 0.3.4), tidyr (>= 1.1.4),
+        digest, rlang, tibble, checkmate (>= 2.0.0), GGally,
+        fontawesome, shinyvalidate, htmltools, RColorBrewer, scales,
+        shinyWidgets, r2d3, stats, Hmisc, base64enc, viridisLite,
+        vegawidget, pROC, gt, utils, precrec, glue
+Depends: R (>= 4.0)
+Date: Tue May 31 12:12:27 2022
+Branch: dev
+ParentCommit: 9edd5ae0b32a3c7afbcf7215187748f310087a8a
+VignetteBuilder: knitr
+Remotes: boehringer-ingelheim/[email protected]

LICENSE

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+Copyright 2024 Boehringer-Ingelheim Pharma GmbH & Co.KG
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+S3method("$",pack_of_constants)
+S3method("[",pack_of_constants)
+S3method("[[",pack_of_constants)
+export(boxplot_UI)
+export(boxplot_server)
+export(corr_hm_UI)
+export(corr_hm_server)
+export(forest_UI)
+export(forest_server)
+export(get_lbl)
+export(get_lbl_robust)
+export(get_lbls)
+export(get_lbls_robust)
+export(lineplot_UI)
+export(lineplot_server)
+export(lp_mean_summary_functions)
+export(lp_median_summary_functions)
+export(mock_app_boxplot)
+export(mock_app_boxplot_mm)
+export(mock_app_corr_hm)
+export(mock_app_correlation_hm_mm)
+export(mock_app_forest)
+export(mock_app_hmcat)
+export(mock_app_hmcont)
+export(mock_app_hmpar)
+export(mock_app_lineplot)
+export(mock_app_scatterplot)
+export(mock_app_scatterplotmatrix)
+export(mock_app_wf)
+export(mock_app_wfphm)
+export(mock_app_wfphm2)
+export(mock_roc_app)
+export(mock_roc_mm_app)
+export(mock_wfphm_mm_app)
+export(mod_boxplot)
+export(mod_boxplot_papo)
+export(mod_corr_hm)
+export(mod_forest)
+export(mod_lineplot)
+export(mod_roc)
+export(mod_scatterplot)
+export(mod_scatterplotmatrix)
+export(mod_wfphm)
+export(odds_ratio)
+export(pearson_correlation)
+export(roc_UI)
+export(roc_server)
+export(scatterplot_UI)
+export(scatterplot_server)
+export(scatterplotmatrix_UI)
+export(scatterplotmatrix_server)
+export(set_lbl)
+export(set_lbls)
+export(spearman_correlation)
+export(spm_subset_data)
+export(tr_gini)
+export(tr_identity)
+export(tr_min_max)
+export(tr_percentize)
+export(tr_trunc_z_score)
+export(tr_z_score)
+export(wfphm_UI)
+export(wfphm_server)
+importFrom(dplyr,.data)
+importFrom(rlang,":=")

NEWS.md

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+# dv.biomarker.general 0.0.4
+
+* Correlation heatmap:
+    * NA and Inf values are removed before the scatterplot to avoid spurious points
+* Lineplot:
+    * Lineplot does no longer crash when dataset is empty
+    * Populates inline titles with column names when labels are not available
+    * Brush selection behaves correctly when sidebar is expanded in dv.manager and it does not crash when the selection
+      is empty
+    * Prevents visit reset when dataset changes in module manager
+
+
+* Migrated Waterfall plus heatmap module to dv.biomarker.general
+* Migrated dv.roc to dv.biomarker.general
+
+# dv.biomarker.general 0.0.3
+
+* Lineplot:
+    * Added summary data listing with aggregated centrality (mean, median, ...) and 
+      dispersion (standard deviation, confidence interval, ...) scores.
+
+* Correlation heatmap:
+    * Selection interface now allows multiple, independent cross-visit and cross-parameter combinations.
+    * Faster plot rendering.
+    * Cleaner graphic output and better management of long axis labels.
+
+# dv.biomarker.general 0.0.2
+
+* Common:
+    * Each module now explicitly specifies the value column used to generate the figures.
+    * Default values are included in all modules.
+    * Menus have been redesigned using shinyvalidate to provide more informative feedback regarding errors or missing selections.
+
+* Boxplot:
+    * Added functionality for saving/loading visualization states.
+
+* Lineplot:
+    * Added functionality for integration with other modules
+    * Supports custom centrality and dispersion measures
+
+* Fix:
+    * Rectified issue where Boxplot added jitter in the y-axis unnecessarily.
+    * Renamed `value_var` to `value_vars` in the Scatter Plot Matrix module to adhere to DV standards.
+    * Improved error handling for correlation calculations in Scatter plot matrix
+
+* Other:
+    * Replaced the magrittr pipeline `%>%` with the base pipeline `|>`.
+    * Resolved the issue with `subset_ds` for single column selections.
+    * Implemented new synthetic datasets in mock_* functions and testing procedures.
+    * Replaced `dv.selector` with locally developed selectors
+
+# dv.biomarker.general 0.0.1
+
+* Initial release with the following modules:
+    * Boxplot: `vignette("boxplot")`
+    * Scatterplot: `vignette("scatterplot")`
+    * Lineplot: `vignette("lineplot")`
+    * Scatterplotmatrix: `vignette("scatterplotmatrix")`
+    * Forest plot: `vignette("forest")`
+    * Scatterplot heatmap plot: `vignette("correlation_heatmap")`

R/aaa_preface.R

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+# THIS FILE IS NAMED aaa_preface.R SO IT IS LOADED BEFORE ALL OTHER FILES
+# DO NOT CHANGE ITS NAME. IT MUST BE THE FIRST ONE ALPHABETICALLY.
+
+#' Build a collection of named constants
+#'
+#' @param ... Named parameters to be collected as constants
+#' @details
+#' Shiny uses strings as IDs to link UI and server elements. E.g:
+#'   foo_UI(id = ns("foo")) ...
+#'   foo_server(id = "foo")
+#'
+#' This pattern makes it easy for programmers to fall on the trap of modifying one instance of the string literal "foo"
+#' without modifying the rest and be unaware of the problem until a bug is hit. It's also easy to mistakes uses of "foo"
+#' as an identifier from other uses (text labels, ...) when, as it's often the case, the parameter is not explicitly
+#' named.
+#' One easy fix consists in using global variables instead of plain string literals. In the case of the previous
+#' example, that would mean:
+#'   ID_FOO <- "foo"
+#'   foo_UI(ns(ID_FOO)) ...
+#'   foo_server(ID_FOO)
+#'
+#' That simple addition makes the purpose of ID_FOO clear and also fails gracefully when not all ID_FOO instances are
+#' updated synchronously along a codebase. It has the drawback of polluting the global namespace with identifier
+#' variables. That's easily solved by creating a container of constants, which is the purpose of this pack_of_constants
+#' alias.
+#'  ID <- pack_of_constants(FOO = "foo", BAR = "bar")
+#'  ID$FOO
+#'  "foo"
+#'  ID$BA
+#'  Error in `$.pack_of_constants`(ID, BA) :
+#'  Pack of constants "ID" does not contain "BA"
+#'
+#' The pack of constants is a plain named list that enforces that all elements have unique, non-null names.
+#' It is tagged as an S3 object to override its extraction operators.
+#'
+#' The use of checkmate is unnecessary, but it's a Good Library(TM) and your module should rely on it anyways
+#' @keywords internal
+pack_of_constants <- function(...) {
+  result <- list(...)
+  checkmate::assert_list(result, any.missing = FALSE, names = "unique")
+  class(result) <- c("pack_of_constants", class(result))
+  result
+}
+
+#' Extract constant from pack
+#'
+#' @param pack pack_of_constants
+#' @param name target constant
+#'
+#' This function differs from the base list extraction method in that it avoids partial matching of keys and throws
+#' an error if the looked-for constant is not contained within the pack.
+#' @keywords internal
+#' @export
+`$.pack_of_constants` <- function(pack, name) {
+  checkmate::assert_true(name %in% names(pack), .var.name = paste0(deparse(substitute(pack)), "$", name))
+  NextMethod()
+}
+
+# This exports are recent requirement for devtools check https://github.com/r-lib/roxygen2/issues/1592#issue-2121199122
+#' @keywords internal
+#' @export
+`[[.pack_of_constants` <- `$.pack_of_constants`
+
+#' @export
+#' @keywords internal
+`[.pack_of_constants` <- function(pack, name) {
+  stop("Invalid pack_of_constants method")
+}
+
+poc <- pack_of_constants