From bddac487fa74ed1054ae43ee3165c3a9ea106cbc Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Fri, 23 Jan 2026 14:55:53 -0800
Subject: [PATCH 1/3] pdf -> html for vignettes

---
 vignettes/ManuscriptFigures.Rmd | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/vignettes/ManuscriptFigures.Rmd b/vignettes/ManuscriptFigures.Rmd
index e45381f..7b728f9 100644
--- a/vignettes/ManuscriptFigures.Rmd
+++ b/vignettes/ManuscriptFigures.Rmd
@@ -2,10 +2,13 @@
 title: 'Reproducing Manuscript Figures'
 date: '`r Sys.Date()`'
 author: 'Helena Winata'
-output: rmarkdown::pdf_document
+output: 
+  html_document:
+    toc: true
+    number_sections: false
 vignette: > 
   %\VignetteIndexEntry{Reproducing Manuscript Figures}
-  %\VignetteEngine{rmarkdown}
+  %\VignetteEngine{knitr::rmarkdown}
   \usepackage[utf8]{inputenc}
 ---
 

From 1f32d4cdacad244cab0737cc1b3971ea97609a59 Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Fri, 23 Jan 2026 15:02:34 -0800
Subject: [PATCH 2/3] add functions to NAMESPACE to remove NOTES

---
 NAMESPACE | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 820e916..031284b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,11 +5,12 @@ import(BoutrosLab.plotting.general)
 
 importFrom("graphics", "par", "strheight", "strwidth")
 importFrom("grDevices", "dev.list", "rainbow")
-importFrom("utils", "read.table", "vi", "head")
-importFrom("stats", "median", "setNames", "aggregate", "reshape")
+importFrom("utils", "read.table", "vi", "head", "tail")
+importFrom("stats", "median", "setNames", "aggregate", "reshape", "rnorm", "runif")
 importFrom(
     "grDevices",
     "col2rgb",
+    "rgb",
     "dev.off",
     "pdf",
     "png",
@@ -17,7 +18,6 @@ importFrom(
     "tiff",
     "colorRampPalette"
     )
-
 export(SRCGrob)
 export(create.phylogenetic.tree)
 export(create.ccf.heatmap)

From 8dc7cec3f1e4f3779459f2d9b738d901ed18d414 Mon Sep 17 00:00:00 2001
From: whelena <hwinata@mednet.ucla.edu>
Date: Fri, 23 Jan 2026 15:13:09 -0800
Subject: [PATCH 3/3] rename 'split.' functions and fix file -> filename NOTE

---
 R/angles.R    | 8 ++++----
 R/save.plot.R | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/angles.R b/R/angles.R
index b732066..bb5ac59 100644
--- a/R/angles.R
+++ b/R/angles.R
@@ -35,7 +35,7 @@ calculate.angles.radial <- function(
                 level.spread <- calculate.level.spread(v$spread[v$id %in% child.ids]);
                 level.total.angle <- total.angle * level.spread;
 
-                angles <- split.equal.angle(
+                angles <- divide.equal.angle(
                     base.total.angle = total.angle,
                     level.total.angle = level.total.angle,
                     child.ids = child.ids,
@@ -55,7 +55,7 @@ calculate.angles.radial <- function(
                 # sort children by complexity
                 child.ids <- v$id[v$id %in% child.ids];
                 # if all children are dendrogram, spread evenly by x distance
-                angles <- split.equal.x.dist(
+                angles <- divide.equal.x.dist(
                     current.node.id = current.node.id,
                     child.ids = child.ids,
                     angles = angles,
@@ -72,7 +72,7 @@ calculate.angles.radial <- function(
     return(angles);
     }
 
-split.equal.angle <- function(
+divide.equal.angle <- function(
     base.total.angle,
     level.total.angle,
     child.ids,
@@ -105,7 +105,7 @@ split.equal.angle <- function(
     return(angles);
     }
 
-split.equal.x.dist <- function(
+divide.equal.x.dist <- function(
     current.node.id,
     child.ids,
     angles,
diff --git a/R/save.plot.R b/R/save.plot.R
index 646b95c..9519753 100644
--- a/R/save.plot.R
+++ b/R/save.plot.R
@@ -10,13 +10,13 @@ save.plot <- function(
     supported.extensions <- c('png', 'pdf', 'tiff', 'svg');
     f <- check.file.extension(filename, supported.extensions, 'tiff');
     if (f$ext == 'png') {
-        png(file = f$name, units = units, res = res, bg = bg, ...);
+        png(filename = f$name, units = units, res = res, bg = bg, ...);
     } else if (f$ext == 'tiff') {
-        tiff(file = f$name, units = units, res = res, bg = bg, ...);
+        tiff(filename = f$name, units = units, res = res, bg = bg, ...);
     } else if (f$ext == 'pdf') {
         pdf(file = f$name, ...);
     } else if (f$ext == 'svg') {
-        svg(file = f$name, bg = bg, ...);
+        svg(filename = f$name, bg = bg, ...);
         }
 
     grid.newpage();