change name of alignment class to ms_alignment

NAMESPACE

@@ -1,12 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(dim,msdial_alignment)
-S3method(head,msdial_alignment)
+S3method(dim,ms_alignment)
+S3method(head,ms_alignment)
 S3method(ms_mirror_plot,data.frame)
-S3method(ms_mirror_plot,msdial_alignment)
-S3method(print,msdial_alignment)
-S3method(row.names,msdial_alignment)
-S3method(tail,msdial_alignment)
+S3method(ms_mirror_plot,ms_alignment)
+S3method(print,ms_alignment)
+S3method(row.names,ms_alignment)
+S3method(tail,ms_alignment)
 export(ms_attach_metadata)
 export(ms_calculate_RIs)
 export(ms_call_msdial)

NEWS.md

@@ -4,6 +4,8 @@
 * 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.
+* Changed the name of the `mzinspectr` alignment object from `msdial_alignment` to `ms_alignment`.
 
 # msdialreadr 0.3.3
 

R/attach_metadata.R

@@ -1,13 +1,13 @@
 #' Attach experimental metadata
 #'
-#' Attaches experimental metadata to `MSDIAL_alignment` object. One of the columns in
+#' Attaches experimental metadata to `ms_alignment` object. One of the columns in
 #' the supplied metadata must match exactly the row names of the peak table.
 #'
 #' @aliases attach_metadata
-#' @param x An `MSDIAL_alignment` object.
+#' @param x A \code{ms_alignment} object.
 #' @param metadata A `data.frame` containing the sample metadata.
 #' @param col The name of the column containing the sample names.
-#' @return A \code{MSDIAL_alignment} object with attached metadata in the \code{
+#' @return A \code{ms_alignment} object with attached metadata in the \code{
 #' $sample_meta} slot.
 #' @author Ethan Bass
 #' @export
@@ -24,7 +24,7 @@ ms_attach_metadata <- function(x, metadata, col){
   if (sum((duplicated(metadata[,col]))) > 0)
     stop(paste("Sample names must be unique. Please check column", sQuote(col),
                "for duplicates."))
-  if (!inherits(x,"msdial_alignment"))
+  if (!inherits(x,"ms_alignment"))
     stop(paste("Provided peak table object must be of class 'x'."))
   meta <- data.frame(rownames(x$tab))
   names(meta) <- col

R/ms_search_gadget.R

@@ -1,7 +1,7 @@
 #' Launch MS search gadget for interactive viewing of spectral matches.
 #' @name ms_search_gadget
 #' @importFrom graphics rasterImage par plot.new
-#' @param data An \code{msdial_alignment} object.
+#' @param data An \code{ms_alignment} object.
 #' @export
 
 ms_search_gadget <- function(data){

R/normalization.R

@@ -2,14 +2,14 @@
 #'
 #' @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 x An \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.
 #' @param QC vector of number(s) to specify samples which average to use as reference
 #' (e.g. QC samples)
 #'
-#' @return A normalized \code{msdial_alignment} object or \code{matrix},
+#' @return A normalized \code{ms_alignment} object or \code{matrix},
 #' according to the input.
 #'
 #' @importFrom stats median
@@ -26,7 +26,7 @@
 
 ms_normalize_pqn <- function(x, ref = c("median", "mean"), QC = NULL) {
   ref <- match.arg(ref, c("median","mean"))
-  if (inherits(x, what = "msdial_alignment")){
+  if (inherits(x, what = "ms_alignment")){
     X <- x$tab
   } else if (class(x) %in% c("data.frame","matrix")){
     X <- x
@@ -61,7 +61,7 @@ ms_normalize_pqn <- function(x, ref = c("median", "mean"), QC = NULL) {
 
   X.norm <- as.data.frame(X.norm)
 
-  if (inherits(x, what = "msdial_alignment")){
+  if (inherits(x, what = "ms_alignment")){
     x$tab <- X.norm
   } else{
     x <- X.norm
@@ -73,13 +73,13 @@ ms_normalize_pqn <- function(x, ref = c("median", "mean"), QC = NULL) {
 #'
 #' 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},
+#' @param x An \code{ms_alignment} object or matrix with rows as samples and features as columns.
+#' @return A normalized \code{ms_alignment} object or \code{matrix},
 #' according to the input.
 #' @export
 
 ms_normalize_tsn <- function(x) {
-  if (inherits(x, what = "msdial_alignment")){
+  if (inherits(x, what = "ms_alignment")){
     X <- x$tab
   } else if (class(x) %in% c("data.frame","matrix")){
     X <- x
@@ -92,7 +92,7 @@ ms_normalize_tsn <- function(x) {
 
   X.norm <- as.data.frame(X.norm)
 
-  if (inherits(x, what = "msdial_alignment")){
+  if (inherits(x, what = "ms_alignment")){
     x$tab <- X.norm
   } else{
     x <- X.norm
@@ -104,18 +104,18 @@ ms_normalize_tsn <- function(x) {
 #'
 #' Normalize by internal standard.
 #'
-#' @param x An \code{msdial_alignment} object or matrix with rows as samples and
+#' @param x An \code{ms_alignment} object or matrix with rows as samples and
 #' features as columns.
 #' @param idx Column index of internal standard.
 #' @param plot_it Logical. Whether to plot ITSD against total peak area.
 #' @importFrom graphics abline legend plot
 #' @importFrom stats lm
 #' @author Ethan Bass
-#' @return A normalized \code{msdial_alignment} object or \code{matrix},
+#' @return A normalized \code{ms_alignment} object or \code{matrix},
 #' according to the input.
 #' @export
 ms_normalize_itsd <- function(x, idx, plot_it = FALSE) {
-  if (inherits(x, what = "msdial_alignment")){
+  if (inherits(x, what = "ms_alignment")){
     X <- x$tab
   } else if (class(x) %in% c("data.frame","matrix")){
     X <- x
@@ -141,7 +141,7 @@ ms_normalize_itsd <- function(x, idx, plot_it = FALSE) {
 
   X.norm <- as.data.frame(X.norm)
 
-  if (inherits(x, what = "msdial_alignment")){
+  if (inherits(x, what = "ms_alignment")){
     x$tab <- X.norm
   } else{
     x <- X.norm
@@ -150,12 +150,12 @@ ms_normalize_itsd <- function(x, idx, plot_it = FALSE) {
 }
 
 #' Subtract blanks
-#' @param x A \code{msdial_alignment} object.
+#' @param x A \code{ms_alignment} object.
 #' @param blanks.idx Indices of blank samples
 #' @param blanks.pattern A string that uniquely identifies blank samples by name
 #' @param what Whether to subtract the mean or median value
 #' @param drop Logical. Whether to drop columns containing only zeros. Defaults to TRUE.
-#' @return A \code{msdial_alignment} object with the mean or median of the blanks
+#' @return A \code{ms_alignment} object with the mean or median of the blanks
 #' subtracted from each peak.
 #' @export
 

R/plot_spectrum.R

@@ -20,7 +20,7 @@
 ms_plot_spectrum <- function(x, col, plot_labels = TRUE, lab_int = 0.2,
                              title = TRUE, type = c("plotly", "base"),
                              scale = FALSE, bar_width = 1, digits = 1, ...){
-  if (inherits(x,"msdial_alignment")){
+  if (inherits(x,"ms_alignment")){
     xx <- x$peak_meta
   } else if (inherits(x, "data.frame") && "EI.spectrum" %in% colnames(x)){
     xx <- x
@@ -152,7 +152,7 @@ ms_mirror_plot.data.frame <- function(x, y, plot_labels = TRUE, type = c("plotly
 }
 
 #' Plot two spectra as a mirror plot.
-#' @param x A \code{msdial_alignment} object.
+#' @param x A \code{ms_alignment} object.
 #' @param cols One or more columns in the peak table \code{tab} to plot.
 #' @param ref A row in the matches slot corresponding to the provided column.
 #' @param type What kind of plot to produce. Either base R (\code{base}) or
@@ -165,10 +165,10 @@ ms_mirror_plot.data.frame <- function(x, y, plot_labels = TRUE, type = c("plotly
 #' @param bar_width Width of bars.
 #' @param match_score Logical. Whether to plot match score or not.
 #' @rdname ms_mirror_plot
-#' @method ms_mirror_plot msdial_alignment
+#' @method ms_mirror_plot ms_alignment
 #' @export
 
-ms_mirror_plot.msdial_alignment <- function(x, cols, ref, type=c("plotly", "base"),
+ms_mirror_plot.ms_alignment <- function(x, cols, ref, type=c("plotly", "base"),
                                          scale = TRUE, plot_labels = TRUE,
                                          lab_int = 0.2, digits = 1,
                                          bar_width = 1, match_score = TRUE, ...){

R/read_alignment.R

@@ -3,7 +3,7 @@
 #' @param format The format of the provided alignment file. Currently, only
 #' MS-DIAL '.txt' files are supported (\code{msdial}).
 #' @importFrom utils read.csv
-#' @return Returns \code{msdial_alignment} object. A list of 3 data.frames,
+#' @return Returns \code{ms_alignment} object. A list of 3 data.frames,
 #' containing peak data (\code{tab}), peak metadata (\code{peak_meta}) and
 #' sample metadata (\code{sample_meta}).
 #' @export
@@ -27,12 +27,12 @@ ms_read_alignment <- function(path, format = c("msdial")){
 
   structure(.Data = list(tab = tab, peak_meta = peak_meta,
                          sample_meta = data.frame(full.name = rownames(tab))),
-            class = "msdial_alignment")
+            class = "ms_alignment")
 }
 
 
 #' Filter alignment by provided indices.
-#' @param x An \code{msdial_alignment} object or matrix with rows as samples and features as columns.
+#' @param x An \code{ms_alignment} object or matrix with rows as samples and features as columns.
 #' @param idx Indices to be retained or excluded according to the value of \code{inverse}.
 #' @param what Which dimension to filter on. Either (\code{rows}) or columns
 #' (\code{cols}).
@@ -60,32 +60,32 @@ ms_filter_alignment <- function(x, idx, what=c("rows","cols"), inverse = FALSE){
 #' @importFrom utils head
 #' @noRd
 #' @export
-head.msdial_alignment <- function(x,...){
+head.ms_alignment <- function(x,...){
   head(x$tab)
 }
 
 #' @importFrom utils tail
 #' @noRd
 #' @export
-tail.msdial_alignment <- function(x,...){
+tail.ms_alignment <- function(x,...){
   tail(x$tab)
 }
 
 #' @noRd
 #' @export
-print.msdial_alignment <- function(x, ...){
+print.ms_alignment <- function(x, ...){
   print(x$tab)
 }
 
 #' @noRd
 #' @export
-dim.msdial_alignment <- function(x){
+dim.ms_alignment <- function(x){
   dim(x$tab)
 }
 
 #' @noRd
 #' @export
-row.names.msdial_alignment <- function(x){
+row.names.ms_alignment <- function(x){
   row.names(x$tab)
 }
 

R/search_spectra.R

@@ -1,4 +1,4 @@
-#' Search spectra in MSDIAL alignment against database
+#' Search spectra in MS alignment against database
 #'
 #' This function can be used to identify peaks in a peak table by matching them
 #' to a spectral database (\code{db}). It takes several arguments that can
@@ -11,7 +11,7 @@
 #' index similarity) when calculating the the total similarity score, which is
 #' used to rank matches.
 #'
-#' @param x An \code{msdial_alignment} object.
+#' @param x An \code{ms_alignment} object.
 #' @param db MSP database. The provided object should be a nested list, where the
 #' sublists contain the following elements: retention indices in an element named
 #' \code{RI} and mass spectra in an element called \code{Spectra}. All other elements
@@ -32,7 +32,7 @@
 #' @param progress_bar Logical. Whether to display progress bar or not.
 #' @note See \href{https://github.com/QizhiSu/mspcompiler}{mspcompiler} for help compiling
 #' an msp database.
-#' @return Returns a modified \code{msdial_alignment} object with database matches
+#' @return Returns a modified \code{ms_alignment} object with database matches
 #' in the \code{matches} slot as a list of data frames. Each \code{data.frame}
 #' will contain the database matches as rows and columns corresponding to the
 #' elements of the database entry (e.g. "Name", "InChIKey", etc.) as well as
@@ -86,7 +86,7 @@ ms_search_spectra <- function(x, db, cols, ..., ri_thresh = 100, spectral_weight
 }
 
 #' Get spectrum from MSDIAL alignment object
-#' @param x An \code{msdial_alignment} object or matrix with rows as samples and features as columns.
+#' @param x An \code{ms_alignment} object or matrix with rows as samples and features as columns.
 #' @param col Index of the feature (column).
 #' @return Returns spectrum as a data.frame with two columns: "mz" and "intensity".
 #' @author Ethan Bass
@@ -105,7 +105,7 @@ ms_get_spectrum <- function(x, col){
 #' @param parallel Logical. Whether to use parallel processing. (This feature
 #' does not work on Windows).
 #' @param mc.cores How many cores to use for parallel processing? Defaults to 2.
-#' @param what What kind of object to return. Either \code{msdial_alignment} object,
+#' @param what What kind of object to return. Either \code{ms_alignment} object,
 #'  (\code{msd}), or \code{data.frame} (\code{df}).
 #' @param progress_bar Logical. Whether to display progress bar or not.
 #' @importFrom pbapply pblapply
@@ -151,9 +151,9 @@ 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/) where it is licensed under
-#' BSD-2 (© 2011-2017, Nathan Dodder). The function was refactored here for
+#' This function is slightly adapted from the \code{SpectrumSimilarity} function
+#' in [OrgMassSpecR](https://orgmassspec.github.io/) where it is licensed under
+#' BSD-2 (© 2011-2017, Nathan Dodder). The function was re-factored here for
 #' increased speed.
 #' @param spec.top data frame containing the experimental spectrum's peak list
 #' with the m/z values in the first column and corresponding intensities in the
@@ -167,11 +167,18 @@ msp_to_dataframe <- function(db){
 #' identification. Expressed as a percent of the maximum intensity.
 #' @param xlim numeric vector of length 2, defining the beginning and ending
 #' values of the x-axis.
-#' @param x.threshold
+#' @param x.threshold numeric value of length 1 specifying the m/z threshold
+#' used for the similarity score calculation. Only peaks with m/z values above
+#' the threshold are used in the calculation. This can be used to exclude noise
+#' and/or non-specific ions at the low end of the spectrum. By default all ions
+#' are used.
 #' @author Nathan G. Dodder
 #' @author Ethan Bass
 spectral_similarity <- function(spec.top, spec.bottom, t = 0.25, b = 10,
                                 xlim = c(50, 1200), x.threshold = 0){
+  if (x.threshold < 0){
+    stop("x.threshold argument must be zero or a positive number")
+  }
   colnames(spec.top) <- c("mz", "intensity")
   spec.top$normalized <- round((spec.top$intensity/max(spec.top$intensity)) * 100)
   spec.top <- spec.top[which(spec.top$mz >= xlim[1] & spec.top$mz <= xlim[2]),]
@@ -192,8 +199,6 @@ spectral_similarity <- function(spec.top, spec.bottom, t = 0.25, b = 10,
   alignment[, c(2, 3)][is.na(alignment[, c(2, 3)])] <- 0
   names(alignment) <- c("mz", "intensity.top", "intensity.bottom")
 
-  if (x.threshold < 0)
-    stop("x.threshold argument must be zero or a positive number")
   alignment <- alignment[alignment[, 1] >= x.threshold, ]
   u <- alignment[, 2]
   v <- alignment[, 3]

R/utils.R

@@ -19,7 +19,7 @@ condense_eispectrum <- function(x){
 }
 
 #' Find peak based on retention time and/or mass
-#' @param x An \code{msdial_alignment} object
+#' @param x An \code{ms_alignment} object
 #' @param rt Retention time
 #' @param mz Quant.mass
 #' @param rt.tol Tolerance for matching retention time
@@ -98,7 +98,7 @@ ms_rt_to_ri <- function(rts, RIs){
 }
 
 #' Convert retention times to retention indices in alignment object.
-#' @param x An \code{msdial_alignment} object.
+#' @param x An \code{ms_alignment} object.
 #' @param Ris A matrix or data.frame containing retention times in column one
 #' and retention indices in column two.
 #' @export