copy bs_icon from bsicons pkg

NAMESPACE

@@ -3,6 +3,7 @@
 export(append_cpg_properties)
 export(assign_classification)
 export(assign_pathogenicity_evidence)
+export(bs_icon2)
 export(check_variant2cancer_phenotype)
 export(combine_novel_and_preclassified)
 export(exclude_vars_by_maf)

R/bsicons.R

@@ -0,0 +1,92 @@
+# Copied from https://github.com/rstudio/bsicons/blob/f7dca31/R/icons.R
+icon_info_mini <- list(
+  name = c(
+    "bullseye",
+    "check-square"
+  ),
+  contents = c(
+    "<path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"></path>\n<path d=\"M8 13A5 5 0 1 1 8 3a5 5 0 0 1 0 10zm0 1A6 6 0 1 0 8 2a6 6 0 0 0 0 12z\"></path>\n<path d=\"M8 11a3 3 0 1 1 0-6 3 3 0 0 1 0 6zm0 1a4 4 0 1 0 0-8 4 4 0 0 0 0 8z\"></path>\n<path d=\"M9.5 8a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z\"></path>",
+    "<path d=\"M14 1a1 1 0 0 1 1 1v12a1 1 0 0 1-1 1H2a1 1 0 0 1-1-1V2a1 1 0 0 1 1-1h12zM2 0a2 2 0 0 0-2 2v12a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"></path>\n<path d=\"M10.97 4.97a.75.75 0 0 1 1.071 1.05l-3.992 4.99a.75.75 0 0 1-1.08.02L4.324 8.384a.75.75 0 1 1 1.06-1.06l2.094 2.093 3.473-4.425a.235.235 0 0 1 .02-.022z\"></path>"
+  )
+)
+
+#' Use Bootstrap icons (as inline SVG)
+#'
+#' Copied from https://github.com/rstudio/bsicons.
+#' @param name The name of the Bootstrap icon. Whitespace is replaced with `-`
+#'   (that way, `"arrow up"` can be used to refer to the "actual name" of
+#'   `"arrow-up"`). For a searchable list of names, see <https://icons.getbootstrap.com/>
+#' @param size Any valid CSS unit defining both the height and width of the
+#'   icon.
+#' @param class Additional CSS classes to add to the `<svg>` element. Consider
+#'   providing Bootstrap 5+ utility classes (e.g., `text-success`) here to
+#'   stylize the icon (but also note that those utility classes will only work
+#'   when Bootstrap 5+ is on the page).
+#' @param title If provided (highly recommended), `a11y` defaults to `"sem"`,
+#'   meaning the title is used for on-hover text and screen reader
+#'   announcements.
+#' @param a11y Cases that distinguish the role of the icon and inform which
+#'   accessibility attributes to be used. Icons can either be `"deco"`
+#'   (decorative, the default case), `"sem"` (semantic), `"none"` (no
+#'   accessibility features). The default, `"auto"`, resolves to `"sem"` if a
+#'   `title` is provided (and `"deco"` otherwise).
+#' @param ... additional CSS properties (e.g., `margin`, `position`, etc.)
+#'   placed on the `<svg>` tag.
+#'
+#' @return An [htmltools::HTML()] string containing the SVG icon.
+#' @export
+bs_icon2 <- function(name, size = "1em", class = NULL, title = NULL,
+                     a11y = c("auto", "deco", "sem", "none"), ...) {
+  if (length(name) != 1) {
+    rlang::abort("The number of icons specified in `name` must be 1.")
+  }
+
+  "%||%" <- function(x, y) {
+    if (is.null(x)) y else x
+  }
+
+  name <- sub("\\s+", "-", tolower(name))
+  idx <- match(name, tolower(icon_info_mini$name))
+  stopifnot(!is.na(idx))
+  svg_children <- icon_info_mini$contents[idx]
+  size <- htmltools::validateCssUnit(size)
+  style_attr <- paste0(
+    "height:", size, ";",
+    "width:", size, ";",
+    "fill:currentColor;",
+    # Better default vertical positioning of icons in a inline context (inspired by fontawesome::fa())
+    "vertical-align:-0.125em;",
+    htmltools::css(...)
+  )
+
+  # Generate accessibility attributes if either of
+  # the "deco" or "sem" cases are chosen
+  a11y <- rlang::arg_match(a11y)
+  a11y_attrs <- ""
+
+  if (a11y == "auto") {
+    a11y <- if (is.null(title)) "deco" else "sem"
+  }
+
+  if (a11y == "deco") {
+    a11y_attrs <- 'aria-hidden="true" role="img" '
+  } else if (a11y == "sem") {
+    title <- title %||% name
+    a11y_attrs <- sprintf(
+      'aria-label="%s" role="img" ',
+      htmltools::htmlEscape(title, attribute = TRUE)
+    )
+  }
+
+  res <- sprintf(
+    '<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" class="bi bi-%s %s" style="%s" %s>%s%s</svg>',
+    name,
+    paste(class, collapse = " "),
+    style_attr,
+    a11y_attrs,
+    if (is.null(title)) "" else paste0("<title>", htmltools::htmlEscape(title), "</title>"),
+    svg_children
+  )
+
+  htmltools::browsable(htmltools::HTML(res))
+}

inst/templates/quarto/cpsr_summary.qmd

@@ -90,23 +90,23 @@ bslib::layout_column_wrap(
       "N = ", 
       cps_report$content$snv_indel$v_stat_cpg$n_p + 
         cps_report$content$snv_indel$v_stat_cpg$n_lp),
-    showcase = bsicons::bs_icon("bullseye"), 
+    showcase = cpsr::bs_icon2("bullseye"),
     theme = bslib::value_box_theme(
       bg = color_lp, fg = "#fff"),
     showcase_layout = "left center"
   ),
   bslib::value_box(
     title = "Genes affected by pathogenic variants",
     value = genes_value_box,
-    showcase = bsicons::bs_icon("bullseye"),
+    showcase = cpsr::bs_icon2("bullseye"),
     theme = bslib::value_box_theme(
       bg = color_lp, fg = "#fff"),
     showcase_layout = "left center"
   ),
   bslib::value_box(
     title = "Secondary findings",
     value = value_sf,
-    showcase = bsicons::bs_icon("bullseye"),
+    showcase = cpsr::bs_icon2("bullseye"),
     theme = bslib::value_box_theme(
       bg = color_sf, fg = "#fff"),
     showcase_layout = "left center"
@@ -119,23 +119,23 @@ bslib::layout_column_wrap(
   bslib::value_box(
     title = "Pre-classified variants (ClinVar)",
     value = paste0("N = ", n_clinvar),
-    showcase = bsicons::bs_icon("check-square"),
+    showcase = cpsr::bs_icon2("check-square"),
     theme = bslib::value_box_theme(
       bg = color_clinvar, fg = "#fff"),
     showcase_layout = "left center"
   ),
   bslib::value_box(
     title = "Novel variants",
     value = paste0("N = ", n_novel),
-    showcase = bsicons::bs_icon("check-square"),
+    showcase = cpsr::bs_icon2("check-square"),
     theme = bslib::value_box_theme(
       bg = color_novel, fg = "#fff"),
     showcase_layout = "left center"
   ),
   bslib::value_box(
     title = "VUS variants",
     value = paste0("N = ", n_vus),
-    showcase = bsicons::bs_icon("check-square"),
+    showcase = cpsr::bs_icon2("check-square"),
     theme = bslib::value_box_theme(
       bg = color_vus, fg = "#fff"),
     showcase_layout = "left center"