Add groupnames,XCMSnExp method (issue #250).

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: xcms
 Version: 3.1.1
-Date: 2017-11-28
+Date: 2018-03-08
 Title: LC/MS and GC/MS Data Analysis
 Author: Colin A. Smith <csmith@scripps.edu>,
     Ralf Tautenhahn <rtautenh@gmail.com>,

R/methods-XCMSnExp.R

@@ -2794,3 +2794,60 @@ setMethod("split", "XCMSnExp", function(x, f,
 c.XCMSnExp <- function(...) {
     .concatenate_XCMSnExp(...)
 }
+
+#' @title Generate unique group (feature) names based on mass and retention time
+#'
+#' @description
+#'
+#' `groupnames` generates names for the identified features from the
+#' correspondence analysis based in their mass and retention time. This
+#' generates feature names that are equivalent to the group names of the *old*
+#' user interface (aka xcms1).
+#'
+#' @param object `XCMSnExp` object containing correspondence results.
+#'
+#' @param mzdec `integer(1)` with the number of decimal places to use for m/z (
+#'     defaults to `0`).
+#'
+#' @param rtdec `integer(1)` with the number of decimal places to use for the
+#'     retention time (defaults to `0`).
+#'
+#' @param template `character` with existing group names whose format should
+#'     be emulated.
+#'
+#' @return `character` with unique names for each feature in `object`. The
+#'     format is `M(m/z)T(time in seconds)`.
+#'
+#' @seealso [XCMSnExp].
+#'
+#' @md
+#' 
+#' @rdname groupnames-XCMSnExp
+setMethod("groupnames", "XCMSnExp", function(object, mzdec = 0, rtdec = 0,
+                                             template = NULL) {
+    if (!hasFeatures(object))
+        stop("No feature data present! Use 'groupChromPeaks' first")
+    if (!missing(template)) {
+        tempsplit <- strsplit(template[1], "[T_]")
+        tempsplit <- strsplit(unlist(tempsplit), "\\.")
+        if (length(tempsplit[[1]]) > 1)
+            mzdec <- nchar(tempsplit[[1]][2])
+        else
+            mzdec <- 0
+        if (length(tempsplit[[2]]) > 1)
+            rtdec <- nchar(tempsplit[[2]][2])
+        else
+            rtdec <- 0
+    }
+    mzfmt <- paste0("%.", mzdec, "f")
+    rtfmt <- paste0("%.", rtdec, "f")
+    gnames <- paste0("M", sprintf(mzfmt, featureDefinitions(object)$mzmed),
+                     "T", sprintf(rtfmt, featureDefinitions(object)$rtmed))
+    if (any(dup <- duplicated(gnames)))
+        for (dupname in unique(gnames[dup])) {
+            dupidx <- which(gnames == dupname)
+            gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx),
+                                    sep = "_")
+        }
+    gnames
+})

inst/NEWS

@@ -5,6 +5,7 @@ NEW FEATURES
 - Reading raw files using xcmsSet or xcmsRaw uses now the automatic file type
   detection feature from mzR.
 - c function to concatenate XCMSnExp objects.
+- groupnames method for XCMSnExp objects (issue #250).
 
 BUG FIXES:
 - Fix #237: findPeaks.MSW was not throwing an error if applied to multi-spectrum

inst/unitTests/runit.XCMSnExp.R

@@ -1547,6 +1547,10 @@ test_split <- function() {
     checkTrue(!all(rtime(tmp[[3]]) == rtime(tmp[[3]], adjusted = FALSE)))
 }
 
+test_groupnames_XCMSnExp <- function() {
+    gn <- groupnames(xod_xgrg)
+    checkException(groupnames(xod_x))
+}
 
 ############################################################
 ## Test getEIC alternatives.