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Merged
tnyamaguchi merged 3 commits into from
Jan 23, 2026
+15 −12
Merged

Make sure everything passes devtools::check() #188

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bddac48
pdf -> html for vignettes
whelena Jan 23, 2026
1f32d4c
add functions to NAMESPACE to remove NOTES
whelena Jan 23, 2026
8dc7cec
rename 'split.' functions and fix file -> filename NOTE
whelena Jan 23, 2026
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6 changes: 3 additions & 3 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -5,19 +5,19 @@ 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",
"svg",
"tiff",
"colorRampPalette"
)

export(SRCGrob)
export(create.phylogenetic.tree)
export(create.ccf.heatmap)
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8 changes: 4 additions & 4 deletions R/angles.R
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Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand Down Expand Up @@ -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,
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6 changes: 3 additions & 3 deletions R/save.plot.R
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Expand Up @@ -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();
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7 changes: 5 additions & 2 deletions vignettes/ManuscriptFigures.Rmd
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Expand Up @@ -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}
---

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