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] 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.}