#27 draft documentation vignettes

.Rbuildignore

@@ -1,3 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^vignettes/articles$

.gitignore

@@ -1 +1,2 @@
 inst/doc
+docs

DESCRIPTION

@@ -32,15 +32,18 @@ Imports:
     openxlsx,
     ospsuite.utils (>= 1.7.0),
     readxl
-Remotes:  
+Remotes: 
     ospsuite=Open-Systems-Pharmacology/OSPSuite-R@*release,
     ospsuite.utils=Open-Systems-Pharmacology/OSPSuite.RUtils@*release
 Suggests: 
     devtools,
+    gt,
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    tidyxl
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 Depends: 
     R (>= 4.1.0)
+Config/Needs/website: rmarkdown

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://www.open-systems-pharmacology.org/OSPSuite.QualificationPlanEditor/
+template:
+  bootstrap: 5
+

inst/excel-display.R

@@ -0,0 +1,74 @@
+#' @title displayExcel
+#' @description
+#' A function that displays an Excel file with its styling
+#' for pkgdown html format using `gt` and `tidyxl` packages
+#' @param excelFile path of Excel file
+#' @param level Section level for the displayed tab
+#' @return Character string
+displayExcel <- function(excelFile, level = 2) {
+  htmlContent <- paste(
+    paste0(rep("#", level), collapse = ""),
+    "Excel Content {.tabset .tabset-pills} \n\n"
+  )
+
+  excelSheets <- readxl::excel_sheets(excelFile)
+  excelFormats <- tidyxl::xlsx_formats(excelFile)
+  excelCells <- tidyxl::xlsx_cells(excelFile)
+  for (excelSheet in excelSheets) {
+    excelData <- openxlsx::readWorkbook(xlsxFile = excelFile, sheet = excelSheet, check.names = FALSE)
+    # Select content for the specific Excel sheet
+    dataCells <- excelCells |>
+      dplyr::filter(.data[["sheet"]] %in% excelSheet) |>
+      dplyr::filter(.data[["col"]] == 1)
+    # Create a list define font and background styles for each row
+    dataStyles <- data.frame(
+      row = dataCells$row - 1,
+      color = excelFormats$local$font$color$rgb[dataCells$local_format_id],
+      fill = excelFormats$local$fill$patternFill$fgColor$rgb[dataCells$local_format_id]
+    ) |>
+      dplyr::mutate(
+        color = paste0("#", substr(.data[["color"]], 3, nchar(.data[["color"]]))),
+        fill = paste0("#", substr(.data[["fill"]], 3, nchar(.data[["fill"]]))),
+        color = ifelse(.data[["color"]] %in% "#NA", "#000000", .data[["color"]]),
+        fill = ifelse(.data[["fill"]] %in% "#NA", "#ffffff", .data[["fill"]])
+      )
+    dataStyles <- split(tail(dataStyles, -1), 1:(nrow(dataStyles) - 1))
+    excelTable <- styleExcelData(excelData, dataStyles)
+
+    htmlContent <- c(
+      htmlContent,
+      paste(
+        paste0(rep("#", level + 1), collapse = ""),
+        excelSheet,
+        "\n\n",
+        gt::as_raw_html(excelTable),
+        "\n\n"
+      )
+    )
+  }
+  return(htmlContent)
+}
+
+#' @title dataWithStyle
+#' @description
+#' A function to apply Excel styles in each row of a data.frame
+#' @param data A data.frame
+#' @param styles A list of `color`, `fill` styles mapped to a `row`
+#' @return A `gt` table
+styleExcelData <- function(data, styles) {
+  gtTable <- gt::gt(data)
+  if(nrow(data)==0){
+    return(gtTable)
+  }
+  for (style in styles) {
+    gtTable <- gtTable |>
+      gt::tab_style(
+        style = list(
+          gt::cell_fill(color = style$fill),
+          gt::cell_text(color = style$color)
+        ),
+        locations = gt::cells_body(rows = style$row)
+      )
+  }
+  return(gtTable)
+}

vignettes/articles/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R