renamed ms_tidy_msdial and fixed bug, v0.3.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: msdialreadr
 Type: Package
 Title: Read and Analyze MS-DIAL Alignment Files 
-Version: 0.3.2
+Version: 0.3.3
 Authors@R: 
     person("Ethan", "Bass", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6175-6739"))

NAMESPACE

@@ -19,6 +19,7 @@ export(ms_normalize_pqn)
 export(ms_normalize_tsn)
 export(ms_plot_spectrum)
 export(ms_read_alignment)
+export(ms_reshape_peaktable)
 export(ms_rt_to_ri)
 export(ms_search_gadget)
 export(ms_search_spectra)

NEWS.md

@@ -1,3 +1,9 @@
+# msdialreadr 0.3.3
+
+* Fixed bug `ms_tidy_msdial` when renaming peaks that are out of order.
+* Renamed `ms_tidy_msdial` to `ms_reshape_peaktable`. The old function name is now deprecated.
+* Made some improvements to documentation.
+
 # msdialreadr 0.3.2
 
 * Added option to for renaming peaks via `ms_tidy_msdial` by providing a named character vector.

R/normalization.R

@@ -1,6 +1,6 @@
 #' @title Probabilistic Quotient Normalization
 #'
-#' @description Performs Probabilistic Quotient Normalization
+#' @description Performs Probabilistic Quotient Normalization on peak table.
 #'
 #' @param x An \code{msdial_alignment} object or matrix with rows as samples and features as columns.
 #' @param ref Reference for normalization: either \code{median} (default) to use
@@ -70,7 +70,9 @@ ms_normalize_pqn <- function(x, ref = c("median", "mean"), QC = NULL) {
 }
 
 #' Total sum normalization
+#'
 #' Divides each row by the sum of the features in that row.
+#'
 #' @param x An \code{msdial_alignment} object or matrix with rows as samples and features as columns.
 #' @return A normalized \code{msdial_alignment} object or \code{matrix},
 #' according to the input.
@@ -98,7 +100,10 @@ ms_normalize_tsn <- function(x) {
   x
 }
 
-#' Normalize by internal standard
+#' Internal standard normalization
+#'
+#' Normalize by internal standard.
+#'
 #' @param x An \code{msdial_alignment} object or matrix with rows as samples and
 #' features as columns.
 #' @param idx Column index of internal standard.

R/tidy_msdial.R

@@ -1,4 +1,7 @@
-#' Convert peak to tidy format for plotting
+#' Reshape peak table
+#'
+#' Convert peak table to tidy format for plotting.
+#'
 #' @param x An MS dial alignment object.
 #' @param peaks A character vector specifying the peaks to include in tidy output.
 #' If the character vector is named, the names of the vector elements will be
@@ -14,8 +17,8 @@
 #' @author Ethan Bass
 #' @export
 
-ms_tidy_msdial <- function(x, peaks, metadata, treatments){
-  if (!missing(treatments)){
+ms_reshape_peaktable <- function(x, peaks, metadata, treatments = NULL){
+  if (!is.null(treatments)){
     .Deprecated("metadata", package="msdialreadr", old = "treatments",
                 msg="The `treatments` argument is deprecated as of msdialreadr v0.3.2.
                 \t Please use the `metadata` argument instead.")
@@ -27,13 +30,38 @@ ms_tidy_msdial <- function(x, peaks, metadata, treatments){
     }
     x$tab <- x$tab[,which(colnames(x$tab) %in% peaks), drop = FALSE]
     if (!is.null(names(peaks))){
-      colnames(x$tab) <- names(peaks)
-      peaks <- names(peaks)
+      colnames(x$tab) <- names(peaks)[match(colnames(x$tab), peaks)]
+      peaks <- colnames(x$tab)
     }
-  x}
+  }
   df <- as.data.frame(x$tab)
   df <- cbind(df, select(x$sample_meta, any_of(metadata)))
   df <- mutate(df, sample = row.names(x))
-  df <- pivot_longer(df, cols = peaks, names_to="peak")
+  df <- pivot_longer(df, cols = peaks, names_to = "peak")
   df
 }
+
+#' Reshape peak table
+#'
+#' Converts peak table to tidy format for plotting. This function is deprecated
+#' as of version \code{0.3.3}. Please use \code{\link{ms_reshape_peaktable}} instead.
+#'
+#' @param x An MS dial alignment object.
+#' @param peaks A character vector specifying the peaks to include in tidy output.
+#' If the character vector is named, the names of the vector elements will be
+#' used in place of the original peak names.
+#' @param metadata A character vector specifying the metadata to include in
+#' 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.
+#' @importFrom dplyr select mutate any_of
+#' @importFrom tidyr pivot_longer
+#' @return If \code{export} is \code{TRUE}, returns spectrum as \code{data.frame}.
+#' Otherwise, no return value.
+#' @author Ethan Bass
+#' @export
+
+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)
+}

README.md

@@ -40,7 +40,7 @@ There are currently several different options for feature normalization, includi
 
 ### Peak identification
 
-There is preliminary support for peak identification by searching a user-provided mass-spectral database through the `ms_search_spectra` function. It takes several parameters, including an ms-dial alignment object (`x`), a spectral database (`db`), the column or columns to identify (`cols`), the maximum retention index shift to exclude a match from consideration (`ri_thresh`), the relative weight to give spectral similarity versus retention index similarity (`spectral_weight`), the number of results to return (`n_results`), and the number of cores to use for parallel processing (`mc.cores`).
+There is preliminary support for peak identification by searching a user-provided mass-spectral database through the `ms_search_spectra` function. The database can be loaded into R from an MSP file using the It takes several parameters, including an ms-dial alignment object (`x`), a spectral database (`db`), the column or columns to identify (`cols`), the maximum retention index shift to exclude a match from consideration (`ri_thresh`), the relative weight to give spectral similarity versus retention index similarity (`spectral_weight`), the number of results to return (`n_results`), and the number of cores to use for parallel processing (`mc.cores`).
 
 To compile a mass spectral database, I recommend using [mspcompiler](https://github.com/QizhiSu/mspcompiler).
 
@@ -52,4 +52,4 @@ Spectra can be plotted using either "base R" graphics or "plotly" graphics using
 
 If you use msdialreadr in published work, please cite it as follows:
 
-Bass, E. (2023). msdialreadr: Read and Analyze MS-DIAL Alignment Files (version 0.3.2).
+Bass, E. (2023). msdialreadr: Read and Analyze MS-DIAL Alignment Files (version 0.3.3).

inst/CITATION

@@ -5,10 +5,10 @@ citEntry(
   title    = "msdialreadr: Read and Analyze MS-DIAL Alignment Files",
   author   = "Ethan Bass",
   year     = "2023",
-  note     = "version 0.3.2",
+  note     = "version 0.3.3",
   url      = "",
   doi      = "",
   textVersion = paste("Bass, E. (2023).",
-        "msdialreadr: Read and Analyze MS-DIAL Alignment Files (version 0.3.2)."
+        "msdialreadr: Read and Analyze MS-DIAL Alignment Files (version 0.3.3)."
         )
   )