feat: treeview() outputs either .rds or .html for all interactive trees

R/treeview.R

@@ -11,12 +11,16 @@
 #' @param lineages A set of lineage names which will be used to subdivide outputs in scatter plots.
 #' @param output_dir Outputs will be saved in this directory. Will create the directory if it does
 #'   not exist.
+#' @param   output_format   Scalar string (either \code{rds} or \code{html}). Which file format
+#'   should the interactive plots be placed? For \code{rds}, the default, a \code{ggtree} or
+#'   \code{ggplot2} object will be placed in an \code{rds} file. For \code{html}, an
+#'   \code{htmlwidget} will be placed in a \code{html} file.
 #' @param heatmap_width,heatmap_lab_offset Width and label-offset parameters for the constructed
 #'   heatmap.
 #'
 #' @importFrom rlang .data
 #'
-#' @return A ggtree plot
+#' @return A \code{ggtree} plot.
 #'
 #' @export
 
@@ -25,8 +29,11 @@ treeview <- function(e0,
                      mutations = c("S:A222V", "S:Y145H", "N:Q9L", "S:E484K"),
                      lineages = c("AY\\.9", "AY\\.43", "AY\\.4\\.2"),
                      output_dir = "treeview",
+                     output_format = c("rds", "html"),
                      heatmap_width = .075,
                      heatmap_lab_offset = -6) {
+  output_format <- match.arg(output_format)
+
   # require logistic growth rate, prevent non-empty
   branch_cols <- unique(c(
     "logistic_growth_rate",
@@ -244,7 +251,8 @@ treeview <- function(e0,
       lgr_trees,
       branch_col = "logistic_growth_rate",
       n_leaves = n_leaves,
-      output_dir = output_dir
+      output_dir = output_dir,
+      output_format = output_format
     )
 
     for (branch_col in setdiff(branch_cols, c("logistic_growth_rate"))) {
@@ -256,7 +264,8 @@ treeview <- function(e0,
         tree_list,
         branch_col = branch_col,
         n_leaves = n_leaves,
-        output_dir = output_dir
+        output_dir = output_dir,
+        output_format = output_format
       )
     }
   })