v0.3.2, updates to ms_tidy_msdial function

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: msdialreadr
 Type: Package
 Title: Read and Analyze MS-DIAL Alignment Files 
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: 
     person("Ethan", "Bass", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6175-6739"))

NEWS.md

@@ -1,3 +1,8 @@
+# msdialreadr 0.3.2
+
+* Added option to for renaming peaks via `ms_tidy_msdial` by providing a named character vector.
+* Deprecated `treatment` argument in `ms_tidy_msdial`, replacing it with new `metadata` argument.
+
 # msdialreadr 0.3.1
 
 * Made rcdk (for rendering structures in `ms_search_gadget`) suggested instead of

R/search_spectra.R

@@ -58,7 +58,7 @@ ms_search_spectra <- function(x, db, cols, ..., ri_thresh = 100, spectral_weight
   if (missing(parallel)){
     parallel <- .Platform$OS.type != "windows"
   }
-  laplee <- laplee <- choose_apply_fnc(progress_bar = progress_bar, cl = mc.cores)
+  laplee <- choose_apply_fnc(progress_bar = progress_bar, cl = mc.cores)
   x$matches[cols] <- laplee(cols, function(col){
     try({
       sp <- ms_get_spectrum(x, col)
@@ -71,7 +71,7 @@ ms_search_spectra <- function(x, db, cols, ..., ri_thresh = 100, spectral_weight
       sp_score <- search_msp(sp, db[idx], ..., what = "scores", parallel = FALSE)
       ri_score <- ri_diff[idx]/ri_thresh
       total_score <- sp_score*spectral_weight + ri_score*(1 - spectral_weight)
-      sel <- order(total_score, decreasing = TRUE)[seq_len(n_results)]
+      sel <- order(total_score, decreasing = TRUE, method="radix")[seq_len(n_results)]
       results <- msp_to_dataframe(db[idx][sel])
       results$spectral_match <- sp_score[sel]
       results$ri_match <- ri_score[sel]
@@ -119,8 +119,8 @@ search_msp <- function(x, db, ..., n_results = 10, parallel, mc.cores = 2,
     parallel <- FALSE
     warning("Parallel processing is not currently available on Windows.")
   }
-  laplee <- laplee <- choose_apply_fnc(progress_bar = progress_bar, cl = mc.cores)
-  sim <- unlist(laplee(seq_along(db), function(i){
+  laplee <- choose_apply_fnc(progress_bar = progress_bar, cl = mc.cores)
+  sim <- unlist(lapply(seq_along(db), function(i){
     db[[i]]$Spectra <- as.data.frame(apply(db[[i]]$Spectra, 2, as.numeric))
     try(spectral_similarity(spec.top = x, spec.bottom = db[[i]]$Spectra, ...))
   }))
@@ -149,6 +149,11 @@ msp_to_dataframe <- function(db){
 }
 
 #' Calculate spectral similarity between two peaks
+#' This function is adapted from the \code{SpectrumSimilarity} function in
+#' [OrgMassSpecR](https://orgmassspec.github.io/) but was optimized for increased
+#' speed.
+#' @author Nathan G. Dodder
+#' @author Ethan Bass
 #' @noRd
 spectral_similarity <- function(spec.top, spec.bottom, t = 0.25, b = 10,
                                 xlim = c(50, 1200), x.threshold = 0){

R/tidy_msdial.R

@@ -1,22 +1,39 @@
 #' Convert peak to tidy format for plotting
-#' @param x An MS dial alignment object
-#' @param peaks Peaks to include in tidy output
-#' @param treatments Treatments to include in tidy output
+#' @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, treatments){
-  df <- as.data.frame(x$tab)
-  if (is.numeric(peaks)){
-    peaks <- colnames(df)[peaks]
+ms_tidy_msdial <- function(x, peaks, metadata, treatments){
+  if (!missing(treatments)){
+    .Deprecated("metadata", package="msdialreadr", old = "treatments",
+                msg="The `treatments` argument is deprecated as of msdialreadr v0.3.2.
+                \t Please use the `metadata` argument instead.")
+    metadata <- treatments
   }
-  df <- select(df, any_of(peaks))
-  df <- cbind(df, select(x$sample_meta, any_of(treatments)))
+  if (!missing(peaks)){
+    if (is.numeric(peaks)){
+      peaks <- colnames(df)[peaks]
+    }
+    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)
+    }
+  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
 }

R/utils.R

@@ -65,10 +65,15 @@ choose_apply_fnc <- function(progress_bar, parallel = FALSE, cl = NULL){
   fn
 }
 
-#' Check for required package
+
+#' Check for suggested package
+#' @author Ethan Bass
 #' @noRd
-check_for_pkg <- function(pkg){
-  if (!requireNamespace(pkg, quietly = TRUE)) {
+check_for_pkg <- function(pkg, return_boolean = FALSE){
+  pkg_exists <- requireNamespace(pkg, quietly = TRUE)
+  if (return_boolean){
+    return(pkg_exists)
+  } else if (!pkg_exists) {
     stop(paste(
       "Package", sQuote(pkg), "must be installed to perform this action:
           try", paste0("`install.packages('", pkg, "')`.")),

README.md

@@ -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 0.3.1).
+Bass, E. (2023). msdialreadr: Read and Analyze MS-DIAL Alignment Files (version 0.3.2).

inst/CITATION

@@ -5,10 +5,10 @@ citEntry(
   title    = "msdialreadr: Read and Analyze MS-DIAL Alignment Files",
   author   = "Ethan Bass",
   year     = "2023",
-  note     = "version 0.3.1",
+  note     = "version 0.3.2",
   url      = "",
   doi      = "",
   textVersion = paste("Bass, E. (2023).",
-        "msdialreadr: Read and Analyze MS-DIAL Alignment Files (version 0.3.1)."
+        "msdialreadr: Read and Analyze MS-DIAL Alignment Files (version 0.3.2)."
         )
   )