Merge pull request #20 from guideflandre/main

Fix error when calling multiple Spectra objects in addFragments

Author: lgatto

NAMESPACE

@@ -16,6 +16,7 @@ export(filterPsmRank)
 export(filterPsmShared)
 export(getAminoAcids)
 export(getAtomicMass)
+export(labelFragments)
 export(makeAdjacencyMatrix)
 export(makePeptideProteinVector)
 export(plotAdjacencyMatrix)

NEWS.md

@@ -1,5 +1,10 @@
 # PSMatch 1.11
 
+## PSMatch 1.11.3
+
+- Deprecated `addFragments`. The use of `labelFragments` is endorsed instead.
+    [PR #20](https://github.com/rformassspectrometry/PSMatch/pull/20)
+
 ## PSMatch 1.11.2
 
 - Replace `calculateFragments` with `calculateFragments2`.

R/PSMatch-package.R

@@ -50,7 +50,7 @@
 #'
 #' The package also provides functionality to calculate ions produced
 #' by the fragmentation of a peptides (see [calculateFragments()]) and
-#' annotated MS2 [Spectra::Spectra()] objects (see [addFragments()]).
+#' annotated MS2 [Spectra::Spectra()] objects (see [labelFragments()]).
 #'
 #' @section Vignettes:
 #'

R/fragments-calculate.R

@@ -379,37 +379,37 @@ setMethod("calculateFragments", c("character", "missing"),
                                    max_mods = Inf) {
     modifiable_positions_var <-
         which(fragment.seq %in% names(variable_modifications))
-
+    
     l <- length(modifiable_positions_var)
-
+    
     ## take the maximum amount of modifications possible
     max_mods <- min(max_mods, l)
-
+    
     if (!length(variable_modifications) || max_mods <= 0)
         return(
             list(setNames(integer(length(fragment.seq)), fragment.seq))
         )
-
+    
     .mod <- function(cmb,
                      seq_split = fragment.seq,
                      var_mods = variable_modifications) {
         m <- setNames(integer(length(seq_split)), seq_split)
         m[cmb] <- var_mods[seq_split[cmb]]
         m
     }
-
+    
     c(
         list(setNames(integer(length(fragment.seq)), fragment.seq)),
         if (length(modifiable_positions_var) == 1)
             lapply(modifiable_positions_var, .mod)
         else
             unlist(
                 lapply(seq_len(max_mods),
-                    function(n)combn(
-                        modifiable_positions_var, n,
-                        FUN = .mod,
-                        simplify = FALSE
-                    )
+                       function(n)combn(
+                           modifiable_positions_var, n,
+                           FUN = .mod,
+                           simplify = FALSE
+                       )
                 ),
                 recursive = FALSE
             )

R/fragments-add.R R/fragments-label.RR/fragments-add.R renamed to R/fragments-label.R

@@ -1,4 +1,9 @@
-##' @title Adds MS2 Fragments
+##' @name labelFragments
+##' 
+##' @title labels MS2 Fragments
+##'
+##' @description
+##' Creates a list of annotations based on `calculateFragments` results.  
 ##'
 ##' @param x An instance of class `Spectra` of length 1, containing a
 ##'     spectra variable `"sequence"` with a `character(1)`
@@ -16,16 +21,17 @@
 ##'     [calculateFragments()] to calculate fragment m/z values to be
 ##'     added to the spectra in `x`.
 ##'
-##' @return Return a `character()` with fragment ion labels.
+##' @return Return a `list()` of `character()` with fragment ion labels. The 
+##' elements are named after the peptide they belong to (variable 
+##' modifications included).
 ##'
 ##' @importFrom MsCoreUtils common
 ##'
 ##' @export
 ##'
-##' @author Johannes Rainer, Sebastian Gibb, Laurent Gatto
+##' @author Johannes Rainer, Guillaume Deflandre, Sebastian Gibb, Laurent Gatto
 ##'
 ##' @examples
-##'
 ##' library("Spectra")
 ##'
 ##' sp <- DataFrame(msLevel = 2L, rtime = 2345, sequence = "SIGFEGDSIGR")
@@ -62,39 +68,57 @@
 ##' sp <- Spectra(sp)
 ##'
 ##' ## The fragment ion labels
-##' addFragments(sp)
+##' labelFragments(sp)
 ##'
 ##' ## Annotate the spectum with the fragment labels
-##' plotSpectra(sp, labels = addFragments, labelPos = 3)
-addFragments <- function(x,
-                         tolerance = 0,
-                         ppm = 20,
-                         ...) {
+##' plotSpectra(sp, labels = labelFragments, labelPos = 3)
+labelFragments <- function(x, tolerance = 0, ppm = 20, ...) {
     stopifnot(requireNamespace("Spectra"))
-    stopifnot(inherits(x, "Spectra"),
-              length(x) == 1)
-    stopifnot("sequence" %in% Spectra::spectraVariables(x))
-    y <- Spectra::spectraData(x)[["sequence"]]
-
-    ## Prepare x and y data
-    x_data <- Spectra::peaksData(x)[[1L]]
-    y_data <- calculateFragments(y, verbose = FALSE, ...)
-    y_data <- y_data[order(y_data$mz), ]
+    stopifnot(inherits(x, "Spectra"))
+    super_labels <- vector("list", length = length(x))
+    k <- integer()
 
-    ## stop if variable modifications used
-    ## Temporary check to allow plotSpectra to work fine
-    ## Will need to be removed once plotSpectra accepts variable modifications
-    ## See issue: https://github.com/rformassspectrometry/Spectra/issues/346
-    stopifnot(length(unique(y_data[["peptide"]])) == 1)
+    for (j in seq_along(x)) {
+        stopifnot("sequence" %in% Spectra::spectraVariables(x[j]))
+        y <- Spectra::spectraData(x[j])[["sequence"]]
+        x_data <- Spectra::peaksData(x[j])[[1L]]
+        y_data <- calculateFragments(y, verbose = FALSE, ...)
+        
+        y_data <- split(y_data, y_data$peptide)
+        
+        labels <- vector("list", length = length(y_data))
+        names(labels) <- names(y_data)
+        
+        for (i in seq_along(y_data)) {
+            k <- c(k, j)
+            y_data[[i]] <- y_data[[i]][order(y_data[[i]]$mz), ]
+            idx <- which(MsCoreUtils::common(x_data[, "mz"], 
+                                             y_data[[i]][, "mz"],
+                                             tolerance = tolerance,
+                                             ppm = ppm))
+            idy <- which(MsCoreUtils::common(y_data[[i]][, "mz"], 
+                                             x_data[, "mz"],
+                                             tolerance = tolerance, 
+                                             ppm = ppm))
+            
+            labels[[i]] <- rep(NA_character_, nrow(x_data))
+            labels[[i]][idx] <- y_data[[i]][idy, "ion"]
+        }
+        super_labels[[j]] <- labels
+    }
+    super_labels <- unlist(super_labels, recursive = FALSE)
+    attr(super_labels, "group") <- k
+    super_labels
+}
 
-    ## Find common peaks and prepare annotations
-    idx <- which(MsCoreUtils::common(x_data[, "mz"], y_data[, "mz"],
-                                     tolerance = tolerance, ppm = ppm))
-    idy <- which(MsCoreUtils::common(y_data[, "mz"], x_data[, "mz"],
-                                     tolerance = tolerance, ppm = ppm))
 
-    ## Prepare labels
-    labels <- rep(NA_character_, nrow(x_data))
-    labels[idx] <- y_data[idy, "ion"]
-    labels
+##' @rdname labelFragments
+##' 
+##' @export 
+##' 
+##' @details
+##' `addFragments` is deprecated and will be made defunct; use `labelFragments` instead.
+addFragments <- function(x, tolerance = 0, ppm = 20, ...) {
+    .Deprecated("labelFragments")
+    labelFragments(x, tolerance, ppm, ...)
 }

man/PSMatch.Rd

@@ -0,0 +1,62 @@
+test_that("labelFragments() works", {
+    library("Spectra")
+    seq <- "PQR"
+    frags <- calculateFragments(seq)
+    o <- order(frags$mz)
+    sp <- DataFrame(msLevel = 2L, rtime = 2345, sequence = seq)
+    sp$mz <- list(frags$mz[o])
+    sp$intensity <- list(rep(1, 7))
+    sp <- Spectra(sp)
+    ## all fragments
+    ans <- labelFragments(sp)[[1]]
+    exp <- frags$ion[o]
+    ## Remove attribute
+    expect_identical(ans[1:length(ans)], exp)
+    ## 2nd fragment missing
+    sp$mz[[1]][2] <- sp$mz[[1]][2] * 1.1
+    exp[2] <- NA
+    ans <- labelFragments(sp)[[1]]
+    expect_identical(ans[1:length(ans)], exp)
+    ## 7th fragment missing
+    sp$mz[[1]][7] <- sp$mz[[1]][7] * 1.1
+    exp[7] <- NA
+    ans <- labelFragments(sp)[[1]]
+    expect_identical(ans[1:length(ans)], exp)
+})
+
+
+test_that("labelFragments() works with multiple Spectra", {
+    library("Spectra")
+    seq <- c("PQR", "ACE")
+    frags_pqr <- calculateFragments(seq)[1:7,]
+    frags_ace <- calculateFragments(seq)[8:13,]
+    o_pqr <- order(frags_pqr$mz)
+    o_ace <- order(frags_ace$mz)
+    sp <- DataFrame(msLevel = c(2L, 2L), rtime = c(2345, 2346), sequence = seq)
+    sp$mz <- c(list(frags_pqr$mz[o_pqr]), list(frags_ace$mz[o_ace]))
+    sp$intensity <- c(list(rep(1, 7)), list(rep(1, 6)))
+    sp <- Spectra(sp)
+    ## all fragments
+    ans <- labelFragments(sp)
+    ## Number of elements equal the possibilities of peptide sequences
+    ## This instance: no mod, 1 mod on Q: 2 possibilities
+    expect_equal(length(ans), 2)
+    expect_identical(names(ans), seq)
+})
+
+test_that("labelFragments() works with modifications", {
+    library("Spectra")
+    seq <- "PQR"
+    frags <- calculateFragments(seq)
+    o <- order(frags$mz)
+    sp <- DataFrame(msLevel = 2L, rtime = 2345, sequence = seq)
+    sp$mz <- list(frags$mz[o])
+    sp$intensity <- list(rep(1, 7))
+    sp <- Spectra(sp)
+    ## all fragments
+    ans <- labelFragments(sp, variable_modifications = c(Q = 45))
+    ## Number of elements equal the possibilities of peptide sequences
+    ## This instance: no mod, 1 mod on Q: 2 possibilities
+    expect_equal(length(ans), 2)
+})
+

man/addFragments.Rd man/labelFragments.Rdman/addFragments.Rd renamed to man/labelFragments.Rd

@@ -102,7 +102,7 @@ plotSpectra(sp5449[2])
 ```
 
 ```{r}
-plotSpectra(sp5449[2], labels = addFragments, labelPos = 3)
+plotSpectra(sp5449[2], labels = labelFragments, labelPos = 3)
 ```
 
 # Session information