@@ -12,6 +12,10 @@ if(getRversion() >= "2.15.1")  utils::globalVariables(c("time", "Transition"))

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

 #' Date: 2019-12-13

 #'

+#' @param XIC_group (list) It is a list of dataframe which has two columns. First column is for time

+#'  and second column indicates intensity.

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

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

 #' @examples

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

 #' runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",

@@ -47,6 +51,20 @@ plotXICgroup <- function(XIC_group, peakAnnot = NULL, Title =NULL){

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

 #' Date: 2019-12-13

 #'

+#' @param analyte (string) An analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.

+#' @param run (string) Name of a mzml file without extension.

+#' @param dataPath (char) Path to mzml and osw directory.

+#' @param maxFdrQuery (numeric) A numeric value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.

+#' @param XICfilter (string) This must be one of the strings "sgolay", "none".

+#' @param SgolayFiltOrd (integer) It defines the polynomial order of filer.

+#' @param SgolayFiltLen (integer) Must be an odd number. It defines the length of filter.

+#' @param runType (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".

+#' @param oswMerged (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.

+#' @param nameCutPattern (string) regex expression to fetch mzML file name from RUN.FILENAME columns of osw files.

+#' @param analyteInGroupLabel (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.

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

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

+#'

 #' @examples

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

 #' run <- "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"

@@ -68,6 +86,8 @@ plotAnalyteXICs <- function(analyte, run, dataPath = ".", maxFdrQuery = 1.0,

 }

 #' Plot an aligned XIC-group.

+#'

+#' @details

 #' x-axis cannot have the same time-values, therefore, x-axis is indecized.

 #'

 #' @importFrom zoo na.locf

@@ -77,6 +97,10 @@ plotAnalyteXICs <- function(analyte, run, dataPath = ".", maxFdrQuery = 1.0,

 #'

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

 #' Date: 2019-12-13

+#' @param XIC_group (list) It is a list of dataframe which has two columns. First column is for time

+#'  and second column indicates intensity.

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

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

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

   intensity <- list()

   # Update intensities with aligned time indices.

@@ -99,6 +123,8 @@ plotSingleAlignedChrom <- function(XIC_group, idx, peakAnnot = NULL){

   return(g)}

 #' Plot aligned XICs group for a specific peptide.

+#'

+#' @description

 #' AlignObjOutput is the output from getAlignObjs fucntion.

 #'

 #' @importFrom ggplot2 geom_vline xlab scale_y_continuous

@@ -110,6 +136,14 @@ plotSingleAlignedChrom <- function(XIC_group, idx, peakAnnot = NULL){

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

 #' Date: 2019-12-13

 #'

+#' @param AlignObj (S4 object)

+#' @param XICs.ref (list) List of extracted ion chromatograms (dataframe) from reference run. The dataframe has two columns: first column is for time

+#'  and second column indicates intensity.

+#' @param XICs.eXp (list) List of extracted ion chromatograms (dataframe) from experiment run.The dataframe has two columns: first column is for time

+#'  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.

+#'

 #' @examples

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

 #' runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",

@@ -174,6 +208,12 @@ getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

 #' 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.

+#' @param plotType This must be one of the strings "All", "onlyUnaligned" and "onlyAligned".

+#' @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 .

+#'

 #' @examples

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

 #' runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",

@@ -230,6 +270,8 @@ 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.

+#'

 #' @examples

 #' library(lattice)

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

@@ -8,6 +8,17 @@ AlignObjOutput is the output from getAlignObjs fucntion.}

 plotAlignedAnalytes(AlignObjOutput, plotType = "All",

   DrawAlignR = FALSE, annotatePeak = FALSE, saveFigs = FALSE)

 }

+\arguments{

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

+

+\item{plotType}{This must be one of the strings "All", "onlyUnaligned" and "onlyAligned".}

+

+\item{DrawAlignR}{(logical) TRUE: ggplot objects will be returned.}

+

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

+

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

+}

 \description{

 Plot aligned XICs group for a specific peptide.

 AlignObjOutput is the output from getAlignObjs fucntion.

@@ -6,6 +6,9 @@

 \usage{

 plotAlignmentPath(AlignObjOutput)

 }

+\arguments{

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

+}

 \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.

@@ -10,6 +10,33 @@ plotAnalyteXICs(analyte, run, dataPath = ".", maxFdrQuery = 1,

   nameCutPattern = "(.*)(/)(.*)", analyteInGroupLabel = FALSE,

   peakAnnot = NULL, Title = NULL)

 }

+\arguments{

+\item{analyte}{(string) An analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.}

+

+\item{run}{(string) Name of a mzml file without extension.}

+

+\item{dataPath}{(char) Path to mzml and osw directory.}

+

+\item{maxFdrQuery}{(numeric) A numeric value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.}

+

+\item{XICfilter}{(string) This must be one of the strings "sgolay", "none".}

+

+\item{SgolayFiltOrd}{(integer) It defines the polynomial order of filer.}

+

+\item{SgolayFiltLen}{(integer) Must be an odd number. It defines the length of filter.}

+

+\item{runType}{(char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".}

+

+\item{oswMerged}{(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.}

+

+\item{nameCutPattern}{(string) regex expression to fetch mzML file name from RUN.FILENAME columns of osw files.}

+

+\item{analyteInGroupLabel}{(logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.}

+

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

+

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

+}

 \description{

 Plot extracted-ion chromatogram.

 }

@@ -2,13 +2,22 @@

 % Please edit documentation in R/visualise_chromatograms.R

 \name{plotSingleAlignedChrom}

 \alias{plotSingleAlignedChrom}

-\title{Plot an aligned XIC-group.

-x-axis cannot have the same time-values, therefore, x-axis is indecized.}

+\title{Plot an aligned XIC-group.}

 \usage{

 plotSingleAlignedChrom(XIC_group, idx, peakAnnot = NULL)

 }

+\arguments{

+\item{XIC_group}{(list) It is a list of dataframe which has two columns. First column is for time

+and second column indicates intensity.}

+

+\item{idx}{(integer) Indices of aligned chromatograms.}

+

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

+}

 \description{

 Plot an aligned XIC-group.

+}

+\details{

 x-axis cannot have the same time-values, therefore, x-axis is indecized.

 }

 \author{

@@ -6,6 +6,14 @@

 \usage{

 plotXICgroup(XIC_group, peakAnnot = NULL, Title = NULL)

 }

+\arguments{

+\item{XIC_group}{(list) It is a list of dataframe which has two columns. First column is for time

+and second column indicates intensity.}

+

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

+

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

+}

 \description{

 Plot Extracted-ion chromatogram group.

 }