From f979d249ee4e6e8996395fe37e9a9abd11c07c01 Mon Sep 17 00:00:00 2001
From: Russ Hyde <russ@jumpingrivers.com>
Date: Tue, 17 Jan 2023 15:40:14 +0000
Subject: [PATCH 1/7] refac: rename treeview() param for specifying sina-plot
 output format

---
 R/plot_cluster_sina.R |  4 ++--
 R/treeview.R          | 10 +++++-----
 man/save_sina_plot.Rd |  4 ++--
 man/treeview.Rd       |  6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/plot_cluster_sina.R b/R/plot_cluster_sina.R
index 8c07f47..e73a15c 100644
--- a/R/plot_cluster_sina.R
+++ b/R/plot_cluster_sina.R
@@ -32,8 +32,8 @@ plot_cluster_sina <- function(pldf,
 #' @param   ggobj   \code{ggplot2} object. Contains the plot that is to be saved.
 #' @param   varx   Scalar string. Which variable is depicted in the plot?
 #' @param   output_dir   File path. The directory where the plot will be stored.
-#' @param   output_format   String (either \code{rds}, \code{html} or both). In which formats should
-#'   the plots be saved?
+#' @param   output_format   String (either \code{rds}, \code{html} or both). Default: both. In
+#'   which file format(s) should the plots be saved?
 #' @param   width_svg,height_svg   The width and height of the plot (only used when
 #'   \code{output_format == "html"}).
 #'
diff --git a/R/treeview.R b/R/treeview.R
index c07237f..96c1cc3 100644
--- a/R/treeview.R
+++ b/R/treeview.R
@@ -11,8 +11,8 @@
 #' @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 sina_output_format String (either \code{rds}, \code{html} or both). In which formats
-#'   should the sina-cluster plots be saved?
+#' @param output_format String (either \code{rds}, \code{html} or both). Default: both. In which
+#'   format(s) should the sina-cluster plots be saved?
 #' @param heatmap_width,heatmap_lab_offset Width and label-offset parameters for the constructed
 #'   heatmap.
 #'
@@ -27,10 +27,10 @@ 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",
-                     sina_output_format = c("rds", "html"),
+                     output_format = c("rds", "html"),
                      heatmap_width = .075,
                      heatmap_lab_offset = -6) {
-  sina_output_format <- match.arg(sina_output_format, several.ok = TRUE)
+  output_format <- match.arg(output_format, several.ok = TRUE)
 
   # require logistic growth rate, prevent non-empty
   branch_cols <- unique(c(
@@ -284,7 +284,7 @@ treeview <- function(e0,
         sina_plot,
         varx = vn,
         output_dir = output_dir,
-        output_format = sina_output_format
+        output_format = output_format
       )
     }
   })
diff --git a/man/save_sina_plot.Rd b/man/save_sina_plot.Rd
index 4eeae30..a394131 100644
--- a/man/save_sina_plot.Rd
+++ b/man/save_sina_plot.Rd
@@ -20,8 +20,8 @@ save_sina_plot(
 
 \item{output_dir}{File path. The directory where the plot will be stored.}
 
-\item{output_format}{String (either \code{rds}, \code{html} or both). In which formats should
-the plots be saved?}
+\item{output_format}{String (either \code{rds}, \code{html} or both). Default: both. In
+which file format(s) should the plots be saved?}
 
 \item{width_svg, height_svg}{The width and height of the plot (only used when
 \code{output_format == "html"}).}
diff --git a/man/treeview.Rd b/man/treeview.Rd
index 987a3e0..01f575e 100644
--- a/man/treeview.Rd
+++ b/man/treeview.Rd
@@ -10,7 +10,7 @@ treeview(
   mutations = c("S:A222V", "S:Y145H", "N:Q9L", "S:E484K"),
   lineages = c("AY\\\\.9", "AY\\\\.43", "AY\\\\.4\\\\.2"),
   output_dir = "treeview",
-  sina_output_format = c("rds", "html"),
+  output_format = c("rds", "html"),
   heatmap_width = 0.075,
   heatmap_lab_offset = -6
 )
@@ -29,8 +29,8 @@ logistic growth rate plot will always be produced.}
 \item{output_dir}{Outputs will be saved in this directory. Will create the directory if it does
 not exist.}
 
-\item{sina_output_format}{String (either \code{rds}, \code{html} or both). In which formats
-should the sina-cluster plots be saved?}
+\item{output_format}{String (either \code{rds}, \code{html} or both). Default: both. In which
+format(s) should the sina-cluster plots be saved?}
 
 \item{heatmap_width, heatmap_lab_offset}{Width and label-offset parameters for the constructed
 heatmap.}

From 475a98ade1aa2eb14de797223149823fcbec3c75 Mon Sep 17 00:00:00 2001
From: Russ Hyde <russ@jumpingrivers.com>
Date: Tue, 6 Dec 2022 16:51:35 +0000
Subject: [PATCH 2/7] feat: save_trees() can output interactive trees to .rds
 or .html

---
 R/plot_tree.R     | 35 +++++++++++++++++++++++++++++------
 man/save_trees.Rd | 14 +++++++++++++-
 2 files changed, 42 insertions(+), 7 deletions(-)

diff --git a/R/plot_tree.R b/R/plot_tree.R
index da0c250..ef53978 100644
--- a/R/plot_tree.R
+++ b/R/plot_tree.R
@@ -85,6 +85,10 @@ create_trees <- function(ggtree_data,
 #' @param   branch_col   Scalar string. The name of the statistic that is under study here (e.g.,
 #'   "logistic_growth_rate" or "clock_outlier"). This name will be used in the output file paths.
 #' @param   output_dir   Scalar string. The directory where the plots will be saved.
+#' @param   output_format   Scalar string (either \code{rds} or \code{html}). Which file format
+#'   should the interactive tree plot be placed? For \code{rds}, the default, a \code{ggtree} object
+#'   will be placed in an \code{rds} file. For \code{html}, an htmlwidget will be placed in a
+#'   \code{html} file.
 #' @param   include_date   Boolean. Should the file-paths include the current date?
 #' @inheritParams   create_trees
 #'
@@ -94,7 +98,10 @@ save_trees <- function(tree_list,
                        branch_col,
                        n_leaves,
                        output_dir,
+                       output_format = c("rds", "html"),
                        include_date = FALSE) {
+  output_format <- match.arg(output_format)
+
   basename_prefix <- if (include_date) {
     glue::glue("tree-{branch_col}-{Sys.Date()}")
   } else {
@@ -103,23 +110,39 @@ save_trees <- function(tree_list,
 
   basenames <- c(
     noninteractive = glue::glue("{basename_prefix}.svg"),
-    interactive = glue::glue("{basename_prefix}.rds")
+    interactive = glue::glue("{basename_prefix}.{output_format}")
   )
   files <- file.path(output_dir, basenames)
   names(files) <- names(basenames)
 
+  plot_height <- max(14, floor(n_leaves / 10))
+
   ggplot2::ggsave(
     tree_list[["noninteractive"]],
     filename = files[["noninteractive"]],
-    height = max(14, floor(n_leaves / 10)),
+    height = plot_height,
     width = 16,
     limitsize = FALSE
   )
 
-  saveRDS(
-    tree_list[["interactive"]],
-    file = files[["interactive"]]
-  )
+  if (output_format == "rds") {
+    saveRDS(
+      tree_list[["interactive"]],
+      file = files[["interactive"]]
+    )
+  } else {
+    widget <- create_widget(
+      tree_list[["interactive"]],
+      width_svg = 15,
+      height_svg = plot_height
+    )
+
+    htmlwidgets::saveWidget(
+      widget,
+      file = files[["interactive"]],
+      title = glue::glue("SARS CoV 2 scan {Sys.Date()}")
+    )
+  }
 
   invisible(files)
 }
diff --git a/man/save_trees.Rd b/man/save_trees.Rd
index 333d689..5bdc76b 100644
--- a/man/save_trees.Rd
+++ b/man/save_trees.Rd
@@ -4,7 +4,14 @@
 \alias{save_trees}
 \title{Save the tree views to files}
 \usage{
-save_trees(tree_list, branch_col, n_leaves, output_dir, include_date = FALSE)
+save_trees(
+  tree_list,
+  branch_col,
+  n_leaves,
+  output_dir,
+  output_format = c("rds", "html"),
+  include_date = FALSE
+)
 }
 \arguments{
 \item{tree_list}{List of \code{ggtree} objects. The "noninteractive" and "interactive"
@@ -17,6 +24,11 @@ entries will be saved to an external file. As generated by \code{create_trees}.}
 
 \item{output_dir}{Scalar string. The directory where the plots will be saved.}
 
+\item{output_format}{Scalar string (either \code{rds} or \code{html}). Which file format
+should the interactive tree plot be placed? For \code{rds}, the default, a \code{ggtree} object
+will be placed in an \code{rds} file. For \code{html}, an htmlwidget will be placed in a
+\code{html} file.}
+
 \item{include_date}{Boolean. Should the file-paths include the current date?}
 }
 \value{

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 3/7] 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

From e40dc26374b03cea9ae3e12f81ed5ead3722429a Mon Sep 17 00:00:00 2001
From: Russ Hyde <russ@jumpingrivers.com>
Date: Tue, 17 Jan 2023 16:42:56 +0000
Subject: [PATCH 4/7] feat: save_trees() can export html, rds or both for
 interactive plots

---
 R/plot_tree.R                   | 34 +++++++++++-------
 man/save_trees.Rd               |  8 ++---
 tests/testthat/test-plot_tree.R | 64 ++++++++++++++++++++++++++++++---
 3 files changed, 85 insertions(+), 21 deletions(-)

diff --git a/R/plot_tree.R b/R/plot_tree.R
index ef53978..3dbfa03 100644
--- a/R/plot_tree.R
+++ b/R/plot_tree.R
@@ -85,10 +85,10 @@ create_trees <- function(ggtree_data,
 #' @param   branch_col   Scalar string. The name of the statistic that is under study here (e.g.,
 #'   "logistic_growth_rate" or "clock_outlier"). This name will be used in the output file paths.
 #' @param   output_dir   Scalar string. The directory where the plots will be saved.
-#' @param   output_format   Scalar string (either \code{rds} or \code{html}). Which file format
-#'   should the interactive tree plot be placed? For \code{rds}, the default, a \code{ggtree} object
-#'   will be placed in an \code{rds} file. For \code{html}, an htmlwidget will be placed in a
-#'   \code{html} file.
+#' @param   output_format   String (either \code{rds} or \code{html} or both). Default: both. Which
+#'   file format(s) should the interactive tree plot(s) be placed? For \code{rds}, a \code{ggtree}
+#'   object will be placed in an \code{rds} file. For \code{html}, a \code{htmlwidget} will be
+#'   placed in a \code{html} file.
 #' @param   include_date   Boolean. Should the file-paths include the current date?
 #' @inheritParams   create_trees
 #'
@@ -100,7 +100,11 @@ save_trees <- function(tree_list,
                        output_dir,
                        output_format = c("rds", "html"),
                        include_date = FALSE) {
-  output_format <- match.arg(output_format)
+  output_format <- match.arg(output_format, several.ok = TRUE)
+  required_filetypes <- c(
+    "noninteractive",
+    c(rds = "interactive_rds", html = "interactive_html")[output_format]
+  )
 
   basename_prefix <- if (include_date) {
     glue::glue("tree-{branch_col}-{Sys.Date()}")
@@ -110,10 +114,14 @@ save_trees <- function(tree_list,
 
   basenames <- c(
     noninteractive = glue::glue("{basename_prefix}.svg"),
-    interactive = glue::glue("{basename_prefix}.{output_format}")
+    interactive_rds = glue::glue("{basename_prefix}.rds"),
+    interactive_html = glue::glue("{basename_prefix}.html")
+  )[required_filetypes]
+
+  files <- setNames(
+    file.path(output_dir, basenames),
+    required_filetypes
   )
-  files <- file.path(output_dir, basenames)
-  names(files) <- names(basenames)
 
   plot_height <- max(14, floor(n_leaves / 10))
 
@@ -125,12 +133,14 @@ save_trees <- function(tree_list,
     limitsize = FALSE
   )
 
-  if (output_format == "rds") {
+  if ("rds" %in% output_format) {
     saveRDS(
       tree_list[["interactive"]],
-      file = files[["interactive"]]
+      file = files[["interactive_rds"]]
     )
-  } else {
+  }
+
+  if ("html" %in% output_format) {
     widget <- create_widget(
       tree_list[["interactive"]],
       width_svg = 15,
@@ -139,7 +149,7 @@ save_trees <- function(tree_list,
 
     htmlwidgets::saveWidget(
       widget,
-      file = files[["interactive"]],
+      file = files[["interactive_html"]],
       title = glue::glue("SARS CoV 2 scan {Sys.Date()}")
     )
   }
diff --git a/man/save_trees.Rd b/man/save_trees.Rd
index 5bdc76b..a140cf7 100644
--- a/man/save_trees.Rd
+++ b/man/save_trees.Rd
@@ -24,10 +24,10 @@ entries will be saved to an external file. As generated by \code{create_trees}.}
 
 \item{output_dir}{Scalar string. The directory where the plots will be saved.}
 
-\item{output_format}{Scalar string (either \code{rds} or \code{html}). Which file format
-should the interactive tree plot be placed? For \code{rds}, the default, a \code{ggtree} object
-will be placed in an \code{rds} file. For \code{html}, an htmlwidget will be placed in a
-\code{html} file.}
+\item{output_format}{String (either \code{rds} or \code{html} or both). Default: both. Which
+file format(s) should the interactive tree plot(s) be placed? For \code{rds}, a \code{ggtree}
+object will be placed in an \code{rds} file. For \code{html}, a \code{htmlwidget} will be
+placed in a \code{html} file.}
 
 \item{include_date}{Boolean. Should the file-paths include the current date?}
 }
diff --git a/tests/testthat/test-plot_tree.R b/tests/testthat/test-plot_tree.R
index c535583..2931518 100644
--- a/tests/testthat/test-plot_tree.R
+++ b/tests/testthat/test-plot_tree.R
@@ -7,9 +7,10 @@ describe("save_trees", {
   )
   branch_col <- "logistic_growth_rate"
 
-  it("creates .svg / .rds files - default: without the current date", {
+  it("creates .svg / .rds / .html files - default: without the current date", {
     td <- withr::local_tempdir(pattern = "no-date-svg")
     output_rds <- file.path(td, glue::glue("tree-{branch_col}.rds"))
+    output_html <- file.path(td, glue::glue("tree-{branch_col}.html"))
     output_svg <- file.path(td, glue::glue("tree-{branch_col}.svg"))
 
     created_files <- save_trees(
@@ -17,17 +18,65 @@ describe("save_trees", {
       branch_col = branch_col, output_dir = td, n_leaves = 100
     )
 
-    expect_equal(
+    expect_mapequal(
+      created_files,
+      c(
+        "noninteractive" = output_svg,
+        "interactive_rds" = output_rds,
+        "interactive_html" = output_html
+      )
+    )
+    expect_true(file.exists(output_svg))
+    expect_true(file.exists(output_html))
+    expect_true(file.exists(output_rds))
+  })
+
+  it("creates interactive html plot 'only' based on output_format argument", {
+    td <- withr::local_tempdir(pattern = "no-date-svg")
+    output_html <- file.path(td, glue::glue("tree-{branch_col}.html"))
+    output_svg <- file.path(td, glue::glue("tree-{branch_col}.svg"))
+    unexpected_rds <- file.path(td, glue::glue("tree-{branch_col}.rds"))
+
+    created_files <- save_trees(
+      tree_list,
+      branch_col = branch_col, output_dir = td, n_leaves = 100,
+      output_format = "html"
+    )
+
+    expect_mapequal(
+      created_files,
+      c("noninteractive" = output_svg, "interactive_html" = output_html)
+    )
+    expect_true(file.exists(output_svg))
+    expect_true(file.exists(output_html))
+    expect_false(file.exists(unexpected_rds))
+  })
+
+  it("creates interactive rds plot 'only' based on output_format argument", {
+    td <- withr::local_tempdir(pattern = "no-date-svg")
+    output_rds <- file.path(td, glue::glue("tree-{branch_col}.rds"))
+    output_svg <- file.path(td, glue::glue("tree-{branch_col}.svg"))
+    unexpected_html <- file.path(td, glue::glue("tree-{branch_col}.html"))
+
+    created_files <- save_trees(
+      tree_list,
+      branch_col = branch_col, output_dir = td, n_leaves = 100,
+      output_format = "rds"
+    )
+
+    expect_mapequal(
       created_files,
-      c("noninteractive" = output_svg, "interactive" = output_rds)
+      c("noninteractive" = output_svg, "interactive_rds" = output_rds)
     )
     expect_true(file.exists(output_svg))
     expect_true(file.exists(output_rds))
+    expect_false(file.exists(unexpected_html))
   })
 
-  it("creates .svg / .rds files - optionally including the current date", {
+  it("creates .svg / .rds / .html files - optionally including the current date", {
     td <- withr::local_tempdir(pattern = "noninteractive-svg")
     output_rds <- file.path(td, glue::glue("tree-{branch_col}-{Sys.Date()}.rds"))
+    output_html <- file.path(td, glue::glue("tree-{branch_col}-{Sys.Date()}.html"))
     output_svg <- file.path(td, glue::glue("tree-{branch_col}-{Sys.Date()}.svg"))
 
     created_files <- save_trees(
@@ -37,9 +86,14 @@ describe("save_trees", {
 
     expect_equal(
       created_files,
-      c("noninteractive" = output_svg, "interactive" = output_rds)
+      c(
+        "noninteractive" = output_svg,
+        "interactive_rds" = output_rds,
+        "interactive_html" = output_html
+      )
     )
     expect_true(file.exists(output_svg))
     expect_true(file.exists(output_rds))
+    expect_true(file.exists(output_html))
   })
 })

From 8ddf13b577a70bf2a6969e7e77dffab1231b224c Mon Sep 17 00:00:00 2001
From: Russ Hyde <russ@jumpingrivers.com>
Date: Tue, 17 Jan 2023 17:21:53 +0000
Subject: [PATCH 5/7] refac: simplify tests for filepaths created by
 save_trees()

---
 tests/testthat/test-plot_tree.R | 107 ++++++++++++++++++--------------
 1 file changed, 59 insertions(+), 48 deletions(-)

diff --git a/tests/testthat/test-plot_tree.R b/tests/testthat/test-plot_tree.R
index 2931518..9ed7596 100644
--- a/tests/testthat/test-plot_tree.R
+++ b/tests/testthat/test-plot_tree.R
@@ -1,3 +1,13 @@
+get_default_filepaths <- function(dir_path, base_name) {
+  filepaths <- c(
+    noninteractive = file.path(dir_path, glue::glue("{base_name}.svg")),
+    interactive_html = file.path(dir_path, glue::glue("{base_name}.html")),
+    interactive_rds = file.path(dir_path, glue::glue("{base_name}.rds"))
+  )
+
+  filepaths
+}
+
 describe("save_trees", {
   tree_list <- list(
     noninteractive = ggplot2::ggplot(),
@@ -6,36 +16,41 @@ describe("save_trees", {
     interactive = ggplot2::ggplot()
   )
   branch_col <- "logistic_growth_rate"
+  default_base_name <- glue::glue("tree-{branch_col}")
+  dated_base_name <- glue::glue("tree-{branch_col}-{Sys.Date()}")
 
   it("creates .svg / .rds / .html files - default: without the current date", {
     td <- withr::local_tempdir(pattern = "no-date-svg")
-    output_rds <- file.path(td, glue::glue("tree-{branch_col}.rds"))
-    output_html <- file.path(td, glue::glue("tree-{branch_col}.html"))
-    output_svg <- file.path(td, glue::glue("tree-{branch_col}.svg"))
+
+    filetypes <- list(
+      expected = c("noninteractive", "interactive_html", "interactive_rds"),
+      unexpected = character(0)
+    )
+
+    default_files <- get_default_filepaths(td, default_base_name)
+    expected_files <- default_files[filetypes$expected]
+    unexpected_files <- default_files[filetypes$unexpected]
 
     created_files <- save_trees(
       tree_list,
       branch_col = branch_col, output_dir = td, n_leaves = 100
     )
 
-    expect_mapequal(
-      created_files,
-      c(
-        "noninteractive" = output_svg,
-        "interactive_rds" = output_rds,
-        "interactive_html" = output_html
-      )
-    )
-    expect_true(file.exists(output_svg))
-    expect_true(file.exists(output_html))
-    expect_true(file.exists(output_rds))
+    expect_mapequal(created_files, expected_files)
+    expect_true(all(file.exists(expected_files)))
   })
 
   it("creates interactive html plot 'only' based on output_format argument", {
     td <- withr::local_tempdir(pattern = "no-date-svg")
-    output_html <- file.path(td, glue::glue("tree-{branch_col}.html"))
-    output_svg <- file.path(td, glue::glue("tree-{branch_col}.svg"))
-    unexpected_rds <- file.path(td, glue::glue("tree-{branch_col}.rds"))
+
+    filetypes <- list(
+      expected = c("noninteractive", "interactive_html"),
+      unexpected = "interactive_rds"
+    )
+
+    default_files <- get_default_filepaths(td, default_base_name)
+    expected_files <- default_files[filetypes$expected]
+    unexpected_files <- default_files[filetypes$unexpected]
 
     created_files <- save_trees(
       tree_list,
@@ -43,20 +58,22 @@ describe("save_trees", {
       output_format = "html"
     )
 
-    expect_mapequal(
-      created_files,
-      c("noninteractive" = output_svg, "interactive_html" = output_html)
-    )
-    expect_true(file.exists(output_svg))
-    expect_true(file.exists(output_html))
-    expect_false(file.exists(unexpected_rds))
+    expect_mapequal(created_files, expected_files)
+    expect_true(all(file.exists(expected_files)))
+    expect_false(any(file.exists(unexpected_files)))
   })
 
   it("creates interactive rds plot 'only' based on output_format argument", {
     td <- withr::local_tempdir(pattern = "no-date-svg")
-    output_rds <- file.path(td, glue::glue("tree-{branch_col}.rds"))
-    output_svg <- file.path(td, glue::glue("tree-{branch_col}.svg"))
-    unexpected_html <- file.path(td, glue::glue("tree-{branch_col}.html"))
+
+    filetypes <- list(
+      expected = c("noninteractive", "interactive_rds"),
+      unexpected = "interactive_html"
+    )
+
+    default_files <- get_default_filepaths(td, default_base_name)
+    expected_files <- default_files[filetypes$expected]
+    unexpected_files <- default_files[filetypes$unexpected]
 
     created_files <- save_trees(
       tree_list,
@@ -64,36 +81,30 @@ describe("save_trees", {
       output_format = "rds"
     )
 
-    expect_mapequal(
-      created_files,
-      c("noninteractive" = output_svg, "interactive_rds" = output_rds)
-    )
-    expect_true(file.exists(output_svg))
-    expect_true(file.exists(output_rds))
-    expect_false(file.exists(unexpected_html))
+    expect_mapequal(created_files, expected_files)
+    expect_true(all(file.exists(expected_files)))
+    expect_false(any(file.exists(unexpected_files)))
   })
 
   it("creates .svg / .rds / .html files - optionally including the current date", {
     td <- withr::local_tempdir(pattern = "noninteractive-svg")
-    output_rds <- file.path(td, glue::glue("tree-{branch_col}-{Sys.Date()}.rds"))
-    output_html <- file.path(td, glue::glue("tree-{branch_col}-{Sys.Date()}.html"))
-    output_svg <- file.path(td, glue::glue("tree-{branch_col}-{Sys.Date()}.svg"))
+
+    filetypes <- list(
+      expected = c("noninteractive", "interactive_html", "interactive_rds"),
+      unexpected = character(0)
+    )
+
+    default_files <- get_default_filepaths(td, dated_base_name)
+    expected_files <- default_files[filetypes$expected]
+    unexpected_files <- default_files[filetypes$unexpected]
 
     created_files <- save_trees(
       tree_list,
       branch_col = branch_col, output_dir = td, n_leaves = 100, include_date = TRUE
     )
 
-    expect_equal(
-      created_files,
-      c(
-        "noninteractive" = output_svg,
-        "interactive_rds" = output_rds,
-        "interactive_html" = output_html
-      )
-    )
-    expect_true(file.exists(output_svg))
-    expect_true(file.exists(output_rds))
-    expect_true(file.exists(output_html))
+    expect_mapequal(created_files, expected_files)
+    expect_true(all(file.exists(expected_files)))
+    expect_false(any(file.exists(unexpected_files)))
   })
 })

From 10979d7ea5662de9c56729dbb250fc258a3b7922 Mon Sep 17 00:00:00 2001
From: Russ Hyde <russ@jumpingrivers.com>
Date: Wed, 18 Jan 2023 10:45:27 +0000
Subject: [PATCH 6/7] chore: bump version

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 7 +++++++
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2133303..01bf0ec 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tfpscanner
 Title: Transmission fitness polymorphism scanner 
-Version: 0.2.1
-Date: 2022-12-06
+Version: 0.2.2
+Date: 2023-01-18
 Author: Erik Volz, Olivia Boyd
 Maintainer: Erik Volz <e.volz@imperial.ac.uk>
 Description: A pipeline for scanning a SARS-CoV-2 phylogeny for clades with outlying growth 
diff --git a/NEWS.md b/NEWS.md
index 6e33998..f69857a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# tfpscanner 0.2.2 _2023-01-18_
+
+- Interactive tree view plots can be saved in either `html` (as an htmlwidget) or `rds` (as a 
+  ggtree object) files
+- Cluster SINA plots and interactive tree view plots are saved as _both_ `html` and `rds` by
+  default
+
 # tfpscanner 0.2.1 _2022-12-06_
 
 - "Cluster sina plot"s can be saved in either `html` (as an htmlwidget) or `rds` (as a ggplot2

From e2e0545d9e5b17342852f0e6f30ba7a63b9fdc16 Mon Sep 17 00:00:00 2001
From: Russ Hyde <russ@jumpingrivers.com>
Date: Wed, 18 Jan 2023 10:48:01 +0000
Subject: [PATCH 7/7] env: use htmlwidgets >= 1.6.0 to fix a bug with pandoc
 paths

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 01bf0ec..815bd5b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,7 +16,7 @@ Imports:
     ggplot2,
     ggtree,
     glue,
-    htmlwidgets,
+    htmlwidgets (>= 1.6.0),
     knitr,
     lubridate,
     mgcv,