@@ -65,6 +65,8 @@ plotXICgroup <- function(XIC_group, peakAnnot = NULL, Title =NULL){

 #' @param peakAnnot (numeric) Peak-apex time.

 #' @param Title (logical) TRUE: name of the list will be displayed as title.

 #'

+#' @return A plot to the current device.

+#'

 #' @examples

 #' dataPath <- system.file("extdata", package = "DIAlignR")

 #' run <- "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"

@@ -101,6 +103,7 @@ plotAnalyteXICs <- function(analyte, run, dataPath = ".", maxFdrQuery = 1.0,

 #'  and second column indicates intensity.

 #' @param idx (integer) Indices of aligned chromatograms.

 #' @param peakAnnot (numeric) Peak-apex time.

+#' @return A plot to the current device.

 plotSingleAlignedChrom <- function(XIC_group, idx, peakAnnot = NULL){

   intensity <- list()

   # Update intensities with aligned time indices.

@@ -143,6 +146,7 @@ plotSingleAlignedChrom <- function(XIC_group, idx, peakAnnot = NULL){

 #'  and second column indicates intensity.

 #' @param refPeakLabel (numeric vector) It contains peak apex, left width and right width.

 #' @param annotatePeak (logical) TRUE: Peak boundaries and apex will be highlighted.

+#' @return A plot to the current device.

 #'

 #' @examples

 #' dataPath <- system.file("extdata", package = "DIAlignR")

@@ -213,6 +217,7 @@ getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

 #' @param DrawAlignR (logical) TRUE: ggplot objects will be returned.

 #' @param annotatePeak (logical) TRUE: Peak boundaries and apex will be highlighted.

 #' @param saveFigs (logical) TRUE: Figures will be saved in AlignedAnalytes.pdf .

+#' @return A plot to the current device.

 #'

 #' @examples

 #' dataPath <- system.file("extdata", package = "DIAlignR")

@@ -271,6 +276,7 @@ plotAlignedAnalytes <- function(AlignObjOutput, plotType = "All", DrawAlignR = F

 #' License: (c) Author (2019) + MIT

 #' Date: 2019-12-13

 #' @param AlignObjOutput (list) The list contains AlignObj, raw XICs for reference and experiment, and reference-peak label.

+#' @return A plot to the current device.

 #'

 #' @examples

 #' library(lattice)

@@ -20,6 +20,9 @@ and second column indicates intensity.}

 \item{annotatePeak}{(logical) TRUE: Peak boundaries and apex will be highlighted.}

 }

+\value{

+A plot to the current device.

+}

 \description{

 AlignObjOutput is the output from getAlignObjs fucntion.

 }

@@ -19,6 +19,9 @@ plotAlignedAnalytes(AlignObjOutput, plotType = "All",

 \item{saveFigs}{(logical) TRUE: Figures will be saved in AlignedAnalytes.pdf .}

 }

+\value{

+A plot to the current device.

+}

 \description{

 Plot aligned XICs group for a specific peptide.

 AlignObjOutput is the output from getAlignObjs fucntion.

@@ -9,6 +9,9 @@ plotAlignmentPath(AlignObjOutput)

 \arguments{

 \item{AlignObjOutput}{(list) The list contains AlignObj, raw XICs for reference and experiment, and reference-peak label.}

 }

+\value{

+A plot to the current device.

+}

 \description{

 Plot aligned path through the similarity matrix. Reference run has indices on X-axis, eXp run has them on Y-axis.

 In getAlignObjs function, objType must be set to medium.

@@ -37,6 +37,9 @@ plotAnalyteXICs(analyte, run, dataPath = ".", maxFdrQuery = 1,

 \item{Title}{(logical) TRUE: name of the list will be displayed as title.}

 }

+\value{

+A plot to the current device.

+}

 \description{

 Plot extracted-ion chromatogram.

 }

@@ -14,6 +14,9 @@ and second column indicates intensity.}

 \item{peakAnnot}{(numeric) Peak-apex time.}

 }

+\value{

+A plot to the current device.

+}

 \description{

 Plot an aligned XIC-group.

 }