From 1b065edfa2073580856fe4d13516742604409c94 Mon Sep 17 00:00:00 2001
From: Russ Hyde <russ@jumpingrivers.com>
Date: Tue, 6 Dec 2022 16:58:02 +0000
Subject: [PATCH] feat: treeview() outputs either .rds or .html (or both) for
 interactive plots

---
 R/treeview.R    | 12 ++++++++----
 man/treeview.Rd |  6 ++++--
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/R/treeview.R b/R/treeview.R
index 96c1cc3..985dac0 100644
--- a/R/treeview.R
+++ b/R/treeview.R
@@ -12,13 +12,15 @@
 #' @param output_dir Outputs will be saved in this directory. Will create the directory if it does
 #'   not exist.
 #' @param output_format String (either \code{rds}, \code{html} or both). Default: both. In which
-#'   format(s) should the sina-cluster plots be saved?
+#'   format(s) should the interactive plots be saved? For \code{rds}, a \code{ggtree} or
+#'   \code{ggplot2} object will be placed in \code{rds} files. For \code{html}, \code{htmlwidget}s
+#'   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
 
@@ -251,7 +253,8 @@ 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"))) {
@@ -263,7 +266,8 @@ 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
       )
     }
   })
diff --git a/man/treeview.Rd b/man/treeview.Rd
index 01f575e..7226756 100644
--- a/man/treeview.Rd
+++ b/man/treeview.Rd
@@ -30,13 +30,15 @@ logistic growth rate plot will always be produced.}
 not exist.}
 
 \item{output_format}{String (either \code{rds}, \code{html} or both). Default: both. In which
-format(s) should the sina-cluster plots be saved?}
+format(s) should the interactive plots be saved? For \code{rds}, a \code{ggtree} or
+\code{ggplot2} object will be placed in \code{rds} files. For \code{html}, \code{htmlwidget}s
+will be placed in a \code{html} file.}
 
 \item{heatmap_width, heatmap_lab_offset}{Width and label-offset parameters for the constructed
 heatmap.}
 }
 \value{
-A ggtree plot
+A \code{ggtree} plot.
 }
 \description{
 This will produce a set of html widgets which will highlight by colour and tooltips statistics