fixes

R/AllGenerics.R

@@ -12,21 +12,21 @@ setGeneric("addParams<-", function(object, value) standardGeneric("addParams<-")
 setGeneric("addProcessHistory", function(object, ...)
     standardGeneric("addProcessHistory"))
 
-#' @aliases adjustRtime ObiwarpParam-class PeakGroupsParam-class LamaParama-class
+#' @aliases adjustRtime ObiwarpParam-class PeakGroupsParam-class
 #'
 #' @title Alignment: Retention time correction methods.
 #'
 #' @description
 #'
 #' The `adjustRtime` method(s) perform retention time correction (alignment)
-#' between chromatograms of different samples/dataset. Alignment is performed by default
-#' on MS level 1 data. Retention times of spectra from other MS levels, if
-#' present, are subsequently adjusted based on the adjusted retention times
-#' of the MS1 spectra. Note that calling `adjustRtime` on a *xcms* result object
-#' will remove any eventually present previous alignment results as well as
-#' any correspondence analysis results. To run a second round of alignment,
-#' raw retention times need to be replaced with adjusted ones using the
-#' [applyAdjustedRtime()] function.
+#' between chromatograms of different samples/dataset. Alignment is performed
+#' by default on MS level 1 data. Retention times of spectra from other MS
+#' levels, if present, are subsequently adjusted based on the adjusted
+#' retention times of the MS1 spectra. Note that calling `adjustRtime` on a
+#' *xcms* result object will remove any eventually present previous alignment
+#' results as well as any correspondence analysis results. To run a second
+#' round of alignment, raw retention times need to be replaced with adjusted
+#' ones using the [applyAdjustedRtime()] function.
 #'
 #' The alignment method can be specified (and configured) using a dedicated
 #' `param` argument.
@@ -100,10 +100,6 @@ setGeneric("addProcessHistory", function(object, ...)
 #' @param BPPARAM parallel processing setup. Defaults to `BPPARAM = bpparam()`.
 #'     See [bpparam()] for details.
 #'
-#' @param bs For `LamaParama`: `character(1)` defining the GAM moothing method.
-#'     (defaults to thin plate; NB: B- and P-splines have been shown to produce
-#'     artefacts).
-#'
 #' @param centerSample \code{integer(1)} defining the index of the center sample
 #'     in the experiment. It defaults to
 #'     \code{floor(median(1:length(fileNames(object))))}. Note that if
@@ -164,16 +160,9 @@ setGeneric("addProcessHistory", function(object, ...)
 #' @param initPenalty For `ObiwarpParam`: `numeric(1)` defining the penalty for
 #'     initiating an alignment (for local alignment only).
 #'
-#' @param lamas For `LamaParama`: `matrix` or `data.frame` with the m/z and
-#'     retention times values of features (as first and second column) from the
-#'     external dataset on which the alignment will be based on.
-#'
 #' @param localAlignment For `ObiwarpParam`: `logical(1)` whether a local
 #'     alignment should be performed instead of the default global alignment.
 #'
-#' @param method For `LamaParama`:`character(1)` with the type of warping.
-#'     Either `method = "gam"` or `method = "loess"` (default).
-#'
 #' @param minFraction For `PeakGroupsParam`: `numeric(1)` between 0 and 1
 #'     defining the minimum required proportion of samples in which peaks for
 #'     the peak group were identified. Peak groups passing this criteria will
@@ -191,12 +180,6 @@ setGeneric("addProcessHistory", function(object, ...)
 #' @param object For `adjustRtime`: an [OnDiskMSnExp()], [XCMSnExp()],
 #'     [MsExperiment()] or [XcmsExperiment()] object.
 #'
-#' @param outlierTolerance For `LamaParama`: `numeric(1)` defining the settings
-#'     for outlier removal during the fitting. By default
-#'     (with `outlierTolerance = 3`), all data points with absolute residuals
-#'     larger than 3 times the mean absolute residual of all data points from
-#'     the first, initial fit, are removed from the final model fit.
-#'
 #' @param param The parameter object defining the alignment method (and its
 #'     setting).
 #'
@@ -206,10 +189,6 @@ setGeneric("addProcessHistory", function(object, ...)
 #'     feature/peak group. The `adjustRtimePeakGroups` method is used by
 #'     default to determine this matrix on the provided `object`.
 #'
-#' @param ppm For `LamaParama`: `numeric(1)` defining the m/z-relative maximal
-#'     allowed difference in m/z between `lamas` and chromatographic peaks. Used
-#'     for the mapping of identified chromatographic peaks and lamas.
-#'
 #' @param response For `ObiwarpParam`: `numeric(1)` defining the
 #'     *responsiveness* of warping with `response = 0` giving linear warping on
 #'     start and end points and `response = 100` warping using all bijective
@@ -219,9 +198,9 @@ setGeneric("addProcessHistory", function(object, ...)
 #'     be used to interpolate corrected retention times for all peak groups.
 #'     Can be either `"loess"` or `"linear"`.
 #'
-#' @param span For `PeakGroupsParam` and `LamaParama`: `numeric(1)` defining
-#'     the degree of smoothing (if `smooth = "loess"` or `method = "loess"`).
-#'     This parameter is passed to the internal call to [loess()].
+#' @param span For `PeakGroupsParam`: `numeric(1)` defining
+#'     the degree of smoothing (if `smooth = "loess"`). This parameter is
+#'     passed to the internal call to [loess()].
 #'
 #' @param subset For `ObiwarpParam` and `PeakGroupsParam`: `integer` with the
 #'     indices of samples within the experiment on which the alignment models
@@ -234,24 +213,10 @@ setGeneric("addProcessHistory", function(object, ...)
 #'     Supported options are `"previous"` and `"average"` (default).
 #'     See *Subset-based alignment* section for details.
 #'
-#' @param tolerance For `LamaParama`: `numeric(1)` defining the absolute
-#'     acceptable difference in m/z between lamas and chromatographic peaks.
-#'     Used for the mapping of identified chromatographic peaks and `lamas`.
-#'
-#' @param toleranceRt For `LamaParama`: `numeric(1)` defining the absolute
-#'     acceptable difference in retention time between lamas and
-#'     chromatographic peaks. Used for the mapping of identified chromatographic
-#'     peaks and `lamas`.
-#'
 #' @param value For all assignment methods: the value to set/replace.
 #'
 #' @param x An `ObiwarpParam`, `PeakGroupsParam` or `LamaParama` object.
 #'
-#' @param zeroWeight For `LamaParama`: `numeric(1)`: defines the weight of the
-#'     first data point (i.e. retention times of the first lama-chromatographic
-#'     peak pair). Values larger than 1 reduce warping problems in the early RT
-#'     range.
-#'
 #' @param ... ignored.
 #'
 #' @return

R/XcmsExperiment.R

@@ -1357,7 +1357,7 @@ setMethod(
         object
 })
 
-#'@rdname adjustRtime
+#'@rdname LamaParama
 setMethod(
     "adjustRtime", signature(object = "XcmsExperiment", param = "LamaParama"),
     function(object, param, BPPARAM = bpparam(), ...) {

R/do_adjustRtime-functions.R

@@ -622,8 +622,9 @@ adjustRtimeSubset <- function(rtraw, rtadj, subset,
 #'
 #' Other functions related to this method:
 #'
-#'  - `LamaParama()`: create the parameter object for alignment using
-#'    `adjustRtime()` function. Is also the input for functions listed below.
+#'  - `LamaParama()`: return the respective the parameter object for alignment
+#'    using `adjustRtime()` function. Is also the input for functions listed
+#'    below.
 #'
 #'  - `matchLamasChromPeaks()`: quickly matches each file's ChromPeaks
 #'    to Lamas, allowing the user to evaluate the matches for each file.
@@ -634,18 +635,71 @@ adjustRtimeSubset <- function(rtraw, rtadj, subset,
 #'  - `matchedRtimes()`: Access the list of `data.frame` saved in the
 #'    `LamaParama` object, generated by the `matchLamasChromPeaks()` function.
 #'
+#'  - `plot()`:plot the chromatographic peaks versus the reference lamas as
+#'     well as the fitting line for the chosen model type. The user can decide
+#'     what file to inspect by specifying the assay number with the parameter
+#'     `assay`
+#'
 #'
 #' @param BPPARAM For `matchLamasChromPeaks()`: parallel processing setup.
 #' Defaults to `BPPARAM = bpparam()`. See [bpparam()] for more information.
 #'
+#' @param bs For `LamaParama()`: `character(1)` defining the GAM smoothing method.
+#'     (defaults to thin plate, `bs = "tp"`)
+#'
+#' @param colPoints For `plot()`: color for the plotting of the datapoint.
+#'
+#' @param colFit For `plot()`: color of the fitting line.
+#'
+#' @param index For `plot()`: `numeric(1)` index of the file that should be
+#'  plotted.
+#'
+#' @param lamas For `LamaParama`: `matrix` or `data.frame` with the m/z and
+#'     retention times values of features (as first and second column) from the
+#'     external dataset on which the alignment will be based on.
+#'
+#'
+#' @param method For `LamaParama`:`character(1)` with the type of warping.
+#'     Either `method = "gam"` or `method = "loess"` (default).
+#'
 #' @param object An object of class `XcmsExperiment` with defined ChromPeaks.
 #'
+#' @param outlierTolerance For `LamaParama`: `numeric(1)` defining the settings
+#'     for outlier removal during the fitting. By default
+#'     (with `outlierTolerance = 3`), all data points with absolute residuals
+#'     larger than 3 times the mean absolute residual of all data points from
+#'     the first, initial fit, are removed from the final model fit.
+#'
 #' @param param An object of class `LamaParama` that will later be used for
 #' adjustment using the `[adjustRtime()]` function.
 #'
-#' @param LamaParama same object that will be passed to the `adjustRtime()`
-#' function. To run this function the `matchLamasChromPeaks()` need to be run
-#' on this first.
+#' @param ppm For `LamaParama`: `numeric(1)` defining the m/z-relative maximal
+#'     allowed difference in m/z between `lamas` and chromatographic peaks. Used
+#'     for the mapping of identified chromatographic peaks and lamas.
+#'
+#' @param span For `LamaParama`: `numeric(1)` defining
+#'     the degree of smoothing (`method = "loess"`). This parameter is passed
+#'     to the internal call to [loess()].
+#'
+#' @param tolerance For `LamaParama`: `numeric(1)` defining the absolute
+#'     acceptable difference in m/z between lamas and chromatographic peaks.
+#'     Used for the mapping of identified chromatographic peaks and `lamas`.
+#'
+#' @param toleranceRt For `LamaParama`: `numeric(1)` defining the absolute
+#'     acceptable difference in retention time between lamas and
+#'     chromatographic peaks. Used for the mapping of identified chromatographic
+#'     peaks and `lamas`.
+#'
+#' @param x For `plot()`: object of class `LamaParama` to be plotted.
+#'
+#' @param xlab,ylab  For `plot()`: x- and y-axis labels.
+#'
+#' @param zeroWeight For `LamaParama`: `numeric(1)`: defines the weight of the
+#'     first data point (i.e. retention times of the first lama-chromatographic
+#'     peak pair). Values larger than 1 reduce warping problems in the early RT
+#'     range.
+#'
+#' @param ... For `plot()`: extra parameters to be passed to the function.
 #'
 #' @return
 #' For `matchLamasChromPeaks()`: A `LamaParama` object with new slot `rtMap`
@@ -671,6 +725,7 @@ adjustRtimeSubset <- function(rtraw, rtadj, subset,
 #' tst <- loadXcmsData("faahko_sub2")
 #'
 #' ## create lamas input from the reference dataset
+#' library(MsExperiment)
 #' f <- sampleData(ref)$sample_type
 #' f[f == "QC"] <- NA
 #' ref <- filterFeatures(ref, PercentMissingFilter(threshold = 0, f = f))
@@ -861,7 +916,7 @@ matchLamasChromPeaks <- function(object, param, BPPARAM = bpparam()){
     if (!hasChromPeaks(object))
         stop("'object' needs to have detected ChromPeaks. ",
              "Run 'findChromPeaks()' first.")
-    f <- as.factor(chromPeaks(object)[, "sample"], levels = seq_along(object))
+    f <- factor(chromPeaks(object)[, "sample"], levels = seq_along(object))
     cp_raw <- split.data.frame(chromPeaks(object)[, c("mz", "rt")], f)
     param@nChromPeaks <- vapply(cp_raw, nrow, numeric(1))
     param@rtMap <- bplapply(cp_raw, FUN = function(x) {
@@ -894,13 +949,7 @@ summarizeLamaMatch <- function(param){
     res
 }
 
-#' @title Perform linear interpolation for unsorted retention time.
-#'
-#' @description
-#' This function performs linear interpolation on the non-sorted parts of an
-#' input vector of retention time. To see more details on the interpolation,
-#' see [approx()]
-#'
+
 #' @param rtime `numeric` vector with the retention times for one file/sample.
 #'
 #' @return vector with sorted retention time.

R/functions-Params.R

@@ -274,7 +274,7 @@ PeakGroupsParam <- function(minFraction = 0.9, extraPeaks = 1,
         subset = as.integer(subset), subsetAdjust = subsetAdjust)
 }
 
-#' @rdname adjustRtime
+#' @rdname LamaParama
 LamaParama <- function(lamas = matrix(ncol = 2, nrow = 0,
                                       dimnames = list(NULL, c("mz", "rt"))),
                        method = c("loess", "gam"),
@@ -284,9 +284,7 @@ LamaParama <- function(lamas = matrix(ncol = 2, nrow = 0,
                        ppm = 20,
                        tolerance = 0,
                        toleranceRt = 5,
-                       bs = "tp",
-                       rtMap = list(),
-                       nChromPeaks = numeric()) {
+                       bs = "tp") {
     method <- match.arg(method)
     if (method == "gam")
         .check_gam_library()
@@ -304,9 +302,7 @@ LamaParama <- function(lamas = matrix(ncol = 2, nrow = 0,
         ppm = ppm,
         tolerance = tolerance,
         toleranceRt = toleranceRt,
-        bs = bs,
-        rtMap = rtMap,
-        nChromPeaks = nChromPeaks)
+        bs = bs)
 }
 
 #' @rdname adjustRtime

R/methods-Params.R

@@ -1252,35 +1252,21 @@ setReplaceMethod("subsetAdjust", "PeakGroupsParam", function(object, value) {
 ############################################################
 ## LamaParama
 
-#' @title Plot summary of information of matching lamas to chromPeaks
-#'
-#' @description
-#' the `plot()` function for `LamaParama` object allows to plot the obs
-#' chromatographic peaks versus the reference lamas as well as the fitting
-#' line for the chosen model type. The user can decide what file to inspect by
-#' specifying the assay number with the parameter `assay`
-#'
-#' @param assay `numeric(1)`, assay that should be plotted.
-#'
-#' @return A plot
-#'
-#' @export
-#'
-#' @noRd
-setMethod("plot", "LamaParama", function(x, index = 1L, colPoints = "#00000060",
-                                         colFit = "#00000080",
-                                         xlab = "Matched Chromatographic peaks",
-                                         ylab = "Lamas",
-                                         main = NULL,...){
-    model <- xcms:::.rt_model(method = param@method,
-                              rt_map= x@rtMap[[index]], span = param@span,
-                              resid_ratio = param@outlierTolerance,
-                              zero_weight = param@zeroWeight,
-                              bs = param@bs)
-    x <- x@rtMap[[index]]
-    plot(x, type = "p", xlab = xlab, ylab = ylab, col = "blue",
-         main = main)
-    points(model, type = "l", col = "black")
+#' @rdname LamaParama
+setMethod("plot", signature(x = "LamaParama"),
+          function(x, index = 1L,
+                   colPoints = "#00000060",
+                   colFit = "#00000080",
+                   xlab = "Matched Chromatographic peaks",
+                   ylab = "Lamas",...){
+    model <- .rt_model(method = x@method,
+                              rt_map= x@rtMap[[index]], span = x@span,
+                              resid_ratio = x@outlierTolerance,
+                              zero_weight = x@zeroWeight,
+                              bs = x@bs)
+    datap <- x@rtMap[[index]]
+    plot(datap, type = "p", xlab = xlab, ylab = ylab, col = colPoints, ...)
+    points(model, type = "l", col = colFit)
 })