add fortify_matrix method for phylo object

Author: Yunuuuu

Diff for: NAMESPACE

@@ -138,6 +138,7 @@ S3method(fortify_matrix,MAF)
 S3method(fortify_matrix,default)
 S3method(fortify_matrix,formula)
 S3method(fortify_matrix,matrix)
+S3method(fortify_matrix,phylo)
 S3method(fortify_matrix,waiver)
 S3method(fortify_upset,list)
 S3method(fortify_upset,matrix)

Diff for: R/align-phylo.R

@@ -181,6 +181,25 @@ AlignPhylo <- ggproto("AlignPhylo", Align,
     summary_align = function(self) c(TRUE, FALSE)
 )
 
+#' @inherit fortify_matrix title
+#' @description This method allows a [`phylo`][ape::as.phylo] object to be
+#' directly input into `stack_discrete()` or `circle_discrete()`. This makes it
+#' possible to add [`align_phylo()`] to the stack independently, as
+#' [`align_phylo()`] requires the layout to have labels.
+#' @return A one-column matrix where the tip labels are the values, and the row
+#' names will also be the tip labels.
+#' @family fortify_matrix methods
+#' @export
+fortify_matrix.phylo <- function(data, ...) {
+    rlang::check_dots_empty()
+    if (is.null(labels <- data$tip_labels)) {
+        cli_abort(
+            "{.arg data} {.cls phylo} object must have tip labels to match the layout data"
+        )
+    }
+    as.matrix(vec_set_names(labels, labels))
+}
+
 #' @inherit fortify_data_frame.default title description
 #' @inheritParams rlang::args_dots_empty
 #' @inheritParams fortify_data_frame.dendrogram

Diff for: R/fortify-matrix.R

@@ -12,6 +12,7 @@
 #' - [`fortify_matrix.default()`]
 #' - [`fortify_matrix.MAF()`]
 #' - [`fortify_matrix.GISTIC()`]
+#' - [`fortify_matrix.phylo()`]
 #' @export
 fortify_matrix <- function(data, ...) {
     UseMethod("fortify_matrix")