refac: width/height of tree-views is specified in treeview() rather t…

…han in (non-exported) save_trees()

This makes the function call for save_trees() more similar to
save_sina_plot(), where the width and height are specified as function
arguments.

R/plot_tree.R

@@ -94,25 +94,24 @@ create_trees <- function(ggtree_data,
 #'   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
+#' @param   height_svg,width_svg   Scalar numeric. Height/width of the generated plots. Passed on to
+#'   `ggplot2::ggsave(..., height, width)` and `ggiraph::girafe(..., height_svg, width_svg)`.
 #'
 #' @return   A named vector containing the file paths that were generated.
 
 save_trees <- function(tree_list,
                        branch_col,
-                       n_leaves,
                        output_dir,
                        output_format = c("rds", "html"),
-                       include_date = FALSE) {
+                       include_date = FALSE,
+                       height_svg = NULL,
+                       width_svg = NULL) {
   output_format <- match.arg(output_format, several.ok = TRUE)
   required_filetypes <- c(
     "noninteractive",
     c(rds = "interactive_rds", html = "interactive_html")[output_format]
   )
 
-  height_svg <- max(14, floor(n_leaves / 10))
-  width_svg <- 16
-
   basename_prefix <- if (include_date) {
     glue::glue("tree-{branch_col}-{Sys.Date()}")
   } else {

R/treeview.R

@@ -250,16 +250,20 @@ treeview <- function(e0,
   }
 
   suppressWarnings({
+    height_svg <- max(14, floor(n_leaves / 10))
+    width_svg <- 16
+
     lgr_trees <- create_trees_curried(
       branch_col = "logistic_growth_rate",
       colour_limits = c(-.5, .5)
     )
     save_trees(
       lgr_trees,
       branch_col = "logistic_growth_rate",
-      n_leaves = n_leaves,
       output_dir = output_dir,
-      output_format = output_format
+      output_format = output_format,
+      height_svg = height_svg,
+      width_svg = width_svg
     )
 
     for (branch_col in setdiff(branch_cols, c("logistic_growth_rate"))) {
@@ -271,9 +275,10 @@ treeview <- function(e0,
       save_trees(
         tree_list,
         branch_col = branch_col,
-        n_leaves = n_leaves,
         output_dir = output_dir,
-        output_format = output_format
+        output_format = output_format,
+        height_svg = height_svg,
+        width_svg = width_svg
       )
     }
   })

inst/WORDLIST

@@ -22,7 +22,9 @@ foreach
 generalised
 ggiraph
 ggplot
+ggsave
 ggtree
+girafe
 grey
 htmlwidget
 htmlwidgets
@@ -61,6 +63,7 @@ stringr
 styler
 sublicense
 summarised
+svg
 svglite
 SystemRequirements
 testthat

tests/testthat/test-plot_tree.R

@@ -33,7 +33,7 @@ describe("save_trees", {
 
     created_files <- save_trees(
       tree_list,
-      branch_col = branch_col, output_dir = td, n_leaves = 100
+      branch_col = branch_col, output_dir = td, width_svg = 16, height_svg = 14
     )
 
     expect_mapequal(created_files, expected_files)
@@ -54,7 +54,7 @@ describe("save_trees", {
 
     created_files <- save_trees(
       tree_list,
-      branch_col = branch_col, output_dir = td, n_leaves = 100,
+      branch_col = branch_col, output_dir = td, width_svg = 16, height_svg = 14,
       output_format = "html"
     )
 
@@ -77,7 +77,7 @@ describe("save_trees", {
 
     created_files <- save_trees(
       tree_list,
-      branch_col = branch_col, output_dir = td, n_leaves = 100,
+      branch_col = branch_col, output_dir = td, width_svg = 16, height_svg = 14,
       output_format = "rds"
     )
 
@@ -100,7 +100,7 @@ describe("save_trees", {
 
     created_files <- save_trees(
       tree_list,
-      branch_col = branch_col, output_dir = td, n_leaves = 100, include_date = TRUE
+      branch_col = branch_col, output_dir = td, width_svg = 16, height_svg = 14, include_date = TRUE
     )
 
     expect_mapequal(created_files, expected_files)