From 460a0b94e6f7861866a01b39527d69ba81bb74ed Mon Sep 17 00:00:00 2001
From: Ethan Bass <ethanbass@gmail.com>
Date: Fri, 22 Dec 2023 16:13:43 -0500
Subject: [PATCH] docs: small changes to docs, whitespace

---
 NEWS.md                     |  2 +-
 R/normalization.R           | 11 ++++++-----
 R/reshape_peaktable.R       |  8 +++++---
 man/ms_normalize_pqn.Rd     |  3 ++-
 man/ms_reshape_peaktable.Rd |  3 ++-
 5 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 3684fa2..15776b0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,7 +4,7 @@
 * Updated `ms_filter_alignment` so it filters matches when removing columns from the peak table.
 * Added titles to mass spectra plots with peak name and retention index or time.
 * Fixed bug in retention index matching algorithm for `ms_search_spectra` function.
-* Added `fixed_levels` argument to `ms_reshape_peaktable` so features can be automatically plotted in the order they are provided by the user.
+* Added `fixed_levels` argument to `ms_reshape_peaktable` so features can be plotted in the order they're provided by the user.
 * Changed the name of the `mzinspectr` alignment object from `msdial_alignment` to `ms_alignment`.
 
 # msdialreadr 0.3.3
diff --git a/R/normalization.R b/R/normalization.R
index 7dcc848..4f550e4 100644
--- a/R/normalization.R
+++ b/R/normalization.R
@@ -2,7 +2,8 @@
 #'
 #' @description Performs Probabilistic Quotient Normalization on peak table.
 #'
-#' @param x An \code{ms_alignment} object or matrix with rows as samples and features as columns.
+#' @param x A \code{ms_alignment} object or matrix with rows as samples and
+#' features as columns.
 #' @param ref Reference for normalization: either \code{median} (default) to use
 #' the overall median of variables as the reference, or \code{mean} to use the
 #' overall average of variables as the reference.
@@ -25,7 +26,7 @@
 #' @export
 
 ms_normalize_pqn <- function(x, ref = c("median", "mean"), QC = NULL) {
-  ref <- match.arg(ref, c("median","mean"))
+  ref <- match.arg(ref, c("median", "mean"))
   if (inherits(x, what = "ms_alignment")){
     X <- x$tab
   } else if (class(x) %in% c("data.frame","matrix")){
@@ -160,7 +161,7 @@ ms_normalize_itsd <- function(x, idx, plot_it = FALSE) {
 #' @export
 
 ms_subtract_blanks <- function(x, blanks.idx, blanks.pattern,
-                            what=c("mean","median"), drop = TRUE){
+                            what=c("mean", "median"), drop = TRUE){
   if (missing(blanks.idx)){
     if (!missing(blanks.pattern)){
       blanks.idx <- grep(blanks.pattern, x$sample_meta$full.name)
@@ -181,13 +182,13 @@ ms_subtract_blanks <- function(x, blanks.idx, blanks.pattern,
   })
 
   # Round any negative nunbers up to 0
-  x.n <- apply(x.n, c(1,2), function(y) max(y,0))
+  x.n <- apply(x.n, c(1, 2), function(y) max(y,0))
 
   # drop 0 columns
   if (drop){
     zeros <- which(colMeans(x.n) == 0)
     if (length(zeros) > 0){
-      x.n <- x.n[,-zeros]
+      x.n <- x.n[, -zeros]
     }
   }
   x.n <- as.data.frame(x.n)
diff --git a/R/reshape_peaktable.R b/R/reshape_peaktable.R
index 881c7aa..434e005 100644
--- a/R/reshape_peaktable.R
+++ b/R/reshape_peaktable.R
@@ -10,7 +10,8 @@
 #' the tidy output.
 #' @param treatments This argument is deprecated as of version 0.3.2. It is
 #' synonymous with the new metadata argument which should be used instead.
-#' @param fixed_levels Fix factor levels of features in the order provided.
+#' @param fixed_levels Logical. Whether to fix factor levels of features in the
+#' order provided. Defaults to \code{TRUE}.
 #' @importFrom dplyr select mutate any_of
 #' @importFrom tidyr pivot_longer
 #' @return If \code{export} is \code{TRUE}, returns spectrum as \code{data.frame}.
@@ -31,7 +32,7 @@ ms_reshape_peaktable <- function(x, peaks, metadata, treatments = NULL,
     if (is.numeric(peaks)){
       peaks <- colnames(df)[peaks]
     }
-    df <- df[,match(peaks,colnames(df)), drop = FALSE]
+    df <- df[, match(peaks, colnames(df)), drop = FALSE]
     if (!is.null(names(peaks))){
       colnames(df) <- names(peaks)
       peaks <- colnames(df)
@@ -69,5 +70,6 @@ ms_reshape_peaktable <- function(x, peaks, metadata, treatments = NULL,
 
 ms_tidy_msdial <- function(x, peaks, metadata, treatments = NULL){
   .Deprecated("ms_reshape_peaktable", package = "tidy_msdial")
-  ms_reshape_peaktable(x=x, peaks = peaks, metadata = metadata, treatments = treatments)
+  ms_reshape_peaktable(x = x, peaks = peaks, metadata = metadata,
+                       treatments = treatments)
 }
diff --git a/man/ms_normalize_pqn.Rd b/man/ms_normalize_pqn.Rd
index 08f5813..536ee1e 100644
--- a/man/ms_normalize_pqn.Rd
+++ b/man/ms_normalize_pqn.Rd
@@ -7,7 +7,8 @@
 ms_normalize_pqn(x, ref = c("median", "mean"), QC = NULL)
 }
 \arguments{
-\item{x}{An \code{ms_alignment} object or matrix with rows as samples and features as columns.}
+\item{x}{A \code{ms_alignment} object or matrix with rows as samples and
+features as columns.}
 
 \item{ref}{Reference for normalization: either \code{median} (default) to use
 the overall median of variables as the reference, or \code{mean} to use the
diff --git a/man/ms_reshape_peaktable.Rd b/man/ms_reshape_peaktable.Rd
index 5f6f063..834d747 100644
--- a/man/ms_reshape_peaktable.Rd
+++ b/man/ms_reshape_peaktable.Rd
@@ -25,7 +25,8 @@ the tidy output.}
 \item{treatments}{This argument is deprecated as of version 0.3.2. It is
 synonymous with the new metadata argument which should be used instead.}
 
-\item{fixed_levels}{Fix factor levels of features in the order provided.}
+\item{fixed_levels}{Logical. Whether to fix factor levels of features in the
+order provided. Defaults to \code{TRUE}.}
 }
 \value{
 If \code{export} is \code{TRUE}, returns spectrum as \code{data.frame}.