@@ -1,17 +1,18 @@

 ## quiets concerns of R CMD check re: the .'s that appear in pipelines

-if(getRversion() >= "2.15.1")  utils::globalVariables(c("time", "Transition"))

+if(getRversion() >= "2.15.1")  utils::globalVariables(c())

+

 #' Plot Extracted-ion chromatogram group.

 #'

 #' @importFrom tidyr gather

-#' @importFrom ggplot2 ggplot ggtitle geom_vline geom_line theme theme_bw aes element_text

+#' @importFrom ggplot2 ggplot ggtitle geom_vline geom_line theme theme_bw aes element_text xlab ylab

 #' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}

 #'

 #' ORCID: 0000-0003-3500-8152

 #'

 #' License: (c) Author (2019) + GPL-3

 #' Date: 2019-12-13

-#'

+#' @importFrom rlang .data

 #' @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.

@@ -21,20 +22,21 @@ if(getRversion() >= "2.15.1")  utils::globalVariables(c("time", "Transition"))

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

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

 #'  "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")

-#' XICs <- getXICs(analytes = "QFNNTDIVLLEDFQK_3", runs = runs, dataPath = dataPath,

-#'  XICfilter = "none")

-#' plotXICgroup(XICs[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][[1]])

+#' XICs <- getXICs(analytes = 4618L, runs = runs, dataPath = dataPath, oswMerged = TRUE)

+#' plotXICgroup(XICs[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]])

+#' XICs <- smoothXICs(XICs[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]],

+#'   type = "sgolay", kernelLen = 13, polyOrd = 4)

+#' plotXICgroup(XICs, Title = "Precursor 4618 \n

+#'  run hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt")

 #'

-#' XICs <- getXICs(analytes = "14299_QFNNTDIVLLEDFQK/3", runs = runs, dataPath = dataPath,

-#'        XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 13, analyteInGroupLabel = TRUE)

-#' plotXICgroup(XICs[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][[1]])

 #' @export

 plotXICgroup <- function(XIC_group, peakAnnot = NULL, Title =NULL){

   df <- do.call("cbind", XIC_group)

   df <- df[,!duplicated(colnames(df))]

   colnames(df) <- c("time", paste("V", 1:(ncol(df)-1), sep=""))

-  df <- gather(df, key = "Transition", value = "Intensity", -time)

-  g <- ggplot(df, aes(time, Intensity, col=Transition)) + geom_line(show.legend = FALSE) + theme_bw()

+  df <- gather(df, key = "Transition", value = "Intensity", -.data$time)

+  g <- ggplot(df, aes(.data$time, .data$Intensity, col=.data$Transition)) +

+    geom_line(show.legend = FALSE) + xlab("time") + ylab("intensity")+ theme_bw()

   if(!is.null(Title)) g <- g + ggtitle(paste0(Title)) + theme(plot.title = element_text(hjust = 0.5))

   if(!is.null(peakAnnot)){

     g <- g + geom_vline(xintercept=peakAnnot, lty="dotted", size = 0.4)

@@ -42,6 +44,7 @@ plotXICgroup <- function(XIC_group, peakAnnot = NULL, Title =NULL){

   return(g)

 }

+

 #' Plot extracted-ion chromatogram.

 #'

 #'

@@ -52,17 +55,15 @@ plotXICgroup <- function(XIC_group, peakAnnot = NULL, Title =NULL){

 #' License: (c) Author (2019) + GPL-3

 #' 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 analyte (integer) an analyte is a PRECURSOR.ID from the osw file.

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

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

+#' @param dataPath (string) 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 XICfilter (string) must be either sgolay, boxcar, gaussian, loess or none.

+#' @param polyOrd (integer) order of the polynomial to be fit in the kernel.

+#' @param kernelLen (integer) number of data-points to consider in the kernel.

 #' @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.

 #'

@@ -71,23 +72,23 @@ plotXICgroup <- function(XIC_group, peakAnnot = NULL, Title =NULL){

 #' @examples

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

 #' run <- "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"

-#' plotAnalyteXICs(analyte = "QFNNTDIVLLEDFQK_3", run, dataPath = dataPath, XICfilter = "none")

-#' plotAnalyteXICs(analyte = "14299_QFNNTDIVLLEDFQK/3", run, dataPath = dataPath,

-#' XICfilter = "sgolay", analyteInGroupLabel = TRUE)

+#' plotAnalyteXICs(analyte = 2474L, run, dataPath = dataPath, oswMerged = TRUE, XICfilter = "none")

+#' plotAnalyteXICs(analyte = 2474L, run, dataPath = dataPath, oswMerged = TRUE, XICfilter = "sgolay")

 #' @export

 plotAnalyteXICs <- function(analyte, run, dataPath = ".", maxFdrQuery = 1.0,

-                            XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 9,

-                            runType = "DIA_proteomics", oswMerged = TRUE, nameCutPattern = "(.*)(/)(.*)",

-                            analyteInGroupLabel = FALSE, peakAnnot = NULL, Title = NULL){

+                            XICfilter = "sgolay", polyOrd = 4, kernelLen = 9,

+                            runType = "DIA_proteomics", oswMerged = TRUE,

+                            peakAnnot = NULL, Title = NULL){

   if((length(run) != 1) | (length(analyte) != 1)){

     return(stop("One analyte and single run are needed."))

   }

   XICs <- getXICs(analytes = analyte, runs = run, dataPath = dataPath, maxFdrQuery = maxFdrQuery,

-                  XICfilter = XICfilter, SgolayFiltOrd = SgolayFiltOrd, SgolayFiltLen = SgolayFiltLen,

-                  runType = runType, oswMerged = oswMerged, nameCutPattern = nameCutPattern, analyteInGroupLabel = analyteInGroupLabel)

-  plotXICgroup(XICs[[run]][[analyte]], peakAnnot, Title)

+                  runType = runType, oswMerged = oswMerged)

+  XICs <- smoothXICs(XICs[[run]][[1]], type=XICfilter, kernelLen = kernelLen, polyOrd = polyOrd)

+  plotXICgroup(XICs, peakAnnot, Title)

 }

+

 #' Plot an aligned XIC-group.

 #'

 #' @details

@@ -111,22 +112,27 @@ plotSingleAlignedChrom <- function(XIC_group, idx, peakAnnot = NULL){

   # Update intensities with aligned time indices.

   for(k in seq_along(XIC_group)){

     mutateInt <- XIC_group[[k]][idx, 2]

-    mutateInt <- na.locf(na.locf(mutateInt, na.rm = FALSE),fromLast = TRUE)

+    mutateInt <- na.locf(na.locf(na.approx(mutateInt, na.rm = FALSE), na.rm = FALSE), fromLast = TRUE)

     intensity[[k]] <- mutateInt

   }

-  #TODO: interpolate mutateT so that it can be plotted on x-axis.

   mutateT <- mapIdxToTime(XIC_group[[1]][, "time"], idx)

+  df <- data.frame(x = which(!is.na(mutateT)), y = mutateT[!is.na(mutateT)] )

+  fit <- lm(y ~ x, df)

+  df <- data.frame(x = which(is.na(mutateT)), y = NA)

+  df$y <- predict(fit, newdata = df)

+  for(i in nrow(df)) mutateT[df$x[i]]  <- df$y[i]

+

   df <- do.call("cbind", intensity)

-  Index <- 1:nrow(df)

-  df <- cbind(Index, as.data.frame(df))

-  df <- gather(df, key = "Transition", value = "Intensity", -Index)

+  df <- cbind(mutateT, as.data.frame(df))

+  df <- gather(df, key = "Transition", value = "Intensity", -mutateT)

   # Plot chromatogram

-  g <- ggplot(df, aes(Index, Intensity, col=Transition)) + geom_line(show.legend = FALSE) + theme_bw()

+  g <- ggplot(df, aes(mutateT, .data$Intensity, col=.data$Transition)) + geom_line(show.legend = FALSE) + theme_bw()

   if(!is.null(peakAnnot)){

     g <- g + geom_vline(xintercept=peakAnnot, lty="dotted", size = 0.4)

   }

   return(g)}

+

 #' Plot aligned XICs group for a specific peptide.

 #'

 #' @description

@@ -150,21 +156,25 @@ plotSingleAlignedChrom <- function(XIC_group, idx, peakAnnot = NULL){

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

 #' @return A plot to the current device.

 #'

+#' @keywords internal

 #' @examples

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

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

 #'  "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")

-#' AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath)

-#' AlignObj <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[1]]

-#' XICs.ref <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[2]]

-#' XICs.eXp <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[3]]

-#' refPeakLabel <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[4]]

-#' @keywords internal

+#' AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath)

+#' AlignObj <- AlignObjOutput[[2]][["4618"]][[1]][["AlignObj"]]

+#' XICs.ref <- AlignObjOutput[[2]][["4618"]][[1]][["ref"]]

+#' XICs.eXp <- AlignObjOutput[[2]][["4618"]][[1]][["eXp"]]

+#' refPeakLabel <- AlignObjOutput[[2]][["4618"]][[1]][["peak"]]

+#' \dontrun{

+#' getAlignedFigs(AlignObj, XICs.ref, XICs.eXp, refPeakLabel)

+#' }

 getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

                                annotatePeak = FALSE){

-  AlignedIndices <- cbind(AlignObj@indexA_aligned, AlignObj@indexB_aligned,

-                          AlignObj@score)

-  colnames(AlignedIndices) <- c("indexAligned.ref", "indexAligned.eXp", "score")

+  AlignedIndices <- cbind(slot(AlignObj, "indexA_aligned"),

+                          slot(AlignObj, "indexB_aligned"))

+  colnames(AlignedIndices) <- c("indexAligned.ref", "indexAligned.eXp")

+  # Do not include gaps in reference run.

   AlignedIndices <- AlignedIndices[(AlignedIndices[,"indexAligned.ref"] != 0L), ]

   AlignedIndices[, 1:2][AlignedIndices[, 1:2] == 0] <- NA

   t.ref <- XICs.ref[[1]][["time"]]

@@ -178,7 +188,7 @@ getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

       geom_vline(xintercept=refPeakLabel$rightWidth[1], lty="dashed", size = 0.1)

   }

-  peXpU <- plotXICgroup(XICs.eXp) + scale_y_continuous(labels = scientific_format(digits = 1)) + xlab("eXp time")

+  peXpU <- plotXICgroup(XICs.eXp) + scale_y_continuous(labels = scientific_format(digits = 1)) + xlab("eXp unaligned time")

   if(annotatePeak){

     peXpU <- peXpU +

       geom_vline(xintercept=t.eXp[which.min(abs(t.ref - refPeakLabel$RT[1]))], lty="dotted", size = 0.3) +

@@ -188,7 +198,7 @@ getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

   ###################### Plot aligned chromatogram ######################################

   peXpA <- plotSingleAlignedChrom(XICs.eXp, idx = AlignedIndices[,"indexAligned.eXp"]) +

-    scale_y_continuous(labels = scientific_format(digits = 1)) + xlab("eXp Aligned index")

+    scale_y_continuous(labels = scientific_format(digits = 1)) + xlab("eXp aligned index")

   if(annotatePeak){

     peXpA <- peXpA +

       geom_vline(xintercept=which.min(abs(t.ref - refPeakLabel$RT[1])),

@@ -204,6 +214,7 @@ getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

   figs

 }

+

 #' Plot aligned XICs group for a specific peptide.

 #' AlignObjOutput is the output from getAlignObjs fucntion.

 #'

@@ -215,9 +226,9 @@ getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

 #' License: (c) Author (2019) + GPL-3

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

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

+#' @param outFile (string) name of the output pdf file.

 #' @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.

@@ -226,42 +237,46 @@ getAlignedFigs <- function(AlignObj, XICs.ref, XICs.eXp, refPeakLabel,

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

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

 #'  "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")

-#' AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath)

+#' AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath)

 #' plotAlignedAnalytes(AlignObjOutput)

 #' @export

-plotAlignedAnalytes <- function(AlignObjOutput, plotType = "All", DrawAlignR = FALSE,

+plotAlignedAnalytes <- function(AlignObjOutput, plotType = "All", outFile = "AlignedAnalytes.pdf",

                                 annotatePeak = FALSE, saveFigs = FALSE){

-  if((length(AlignObjOutput) > 1) | saveFigs){

-    grDevices::pdf("AlignedAnalytes.pdf")

+  if((length(AlignObjOutput[[2]][[1]]) > 1) | length(AlignObjOutput[[2]]) > 1 | saveFigs){

+    grDevices::pdf(outFile)

   }

-  for(i in seq_along(AlignObjOutput)){

-    if(is.null(AlignObjOutput[[i]])){

+  # Get fileInfo (output of getRunNames)

+  vec <- AlignObjOutput[[1]][,"runName"]

+  names(vec) <- rownames(AlignObjOutput[[1]])

+  # Iterate over each precursor, check if it is NULL.

+  for(i in seq_along(AlignObjOutput[[2]])){

+    if(is.null(AlignObjOutput[[2]][[i]])){

       next

     }

-    AlignObj <- AlignObjOutput[[i]][[1]]

-    XICs.ref <- AlignObjOutput[[i]][[2]]

-    XICs.eXp <- AlignObjOutput[[i]][[3]]

-    refPeakLabel <- AlignObjOutput[[i]][[4]]

-    analyte <- names(AlignObjOutput)[i]

-    refRun <- names(AlignObjOutput[[i]])[2]

-    eXpRun <- names(AlignObjOutput[[i]])[3]

-    figs <- getAlignedFigs(AlignObj, XICs.ref, XICs.eXp, refPeakLabel, annotatePeak)

-

-    if(DrawAlignR){

-      return(figs)}

+    pairs <- names(AlignObjOutput[[2]][[i]])

+    for(pair in pairs){

+      refRun <- strsplit(pair, split = "_")[[1]][1]

+      eXpRun <- strsplit(pair, split = "_")[[1]][2]

+      AlignObj <- AlignObjOutput[[2]][[i]][[pair]][["AlignObj"]]

+      XICs.ref <- AlignObjOutput[[2]][[i]][[pair]][["ref"]]

+      XICs.eXp <- AlignObjOutput[[2]][[i]][[pair]][["eXp"]]

+      refPeakLabel <- AlignObjOutput[[2]][[i]][[pair]][["peak" ]]

-    if(plotType == "onlyAligned"){

-      grid.arrange(figs[["prefU"]], figs[["peXpA"]], nrow=2, ncol=1,

-                   top = paste0(analyte,"\n", "ref: ", refRun, "\n", "eXp: ", eXpRun ))

-    } else if(plotType == "onlyUnaligned"){

-      grid.arrange(figs[["prefU"]], figs[["peXpU"]], nrow=2, ncol=1,

-                   top = paste0(analyte,"\n", "ref: ", refRun, "\n", "eXp: ", eXpRun ))

-    } else{

-      grid.arrange(figs[["peXpU"]], figs[["prefU"]], figs[["peXpA"]],

-                   nrow=3, ncol=1, top = paste0(analyte,"\n", "ref: ", refRun, "\n", "eXp: ", eXpRun ))

+      analyte <- names(AlignObjOutput[[2]])[i]

+      figs <- getAlignedFigs(AlignObj, XICs.ref, XICs.eXp, refPeakLabel, annotatePeak)

+      if(plotType == "onlyAligned"){

+        grid.arrange(figs[["prefU"]], figs[["peXpA"]], nrow=2, ncol=1,

+                     top = paste0(analyte,"\n", "ref: ", refRun, "\n", "eXp: ", eXpRun ))

+      } else if(plotType == "onlyUnaligned"){

+        grid.arrange(figs[["prefU"]], figs[["peXpU"]], nrow=2, ncol=1,

+                     top = paste0(analyte,"\n", "ref: ", refRun, "\n", "eXp: ", eXpRun ))

+      } else{

+        grid.arrange(figs[["prefU"]], figs[["peXpA"]], figs[["peXpU"]],

+                     nrow=3, ncol=1, top = paste0(analyte,"\n", "ref: ", vec[[refRun]], "\n", "eXp: ", vec[[eXpRun]] ))

+      }

     }

   }

-  if((length(AlignObjOutput) > 1) | saveFigs){

+  if((length(AlignObjOutput[[2]][[1]]) > 1) | length(AlignObjOutput[[2]]) > 1 | saveFigs){

     grDevices::dev.off()

   }

 }

@@ -286,16 +301,22 @@ plotAlignedAnalytes <- function(AlignObjOutput, plotType = "All", DrawAlignR = F

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

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

 #'  "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")

-#' AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath,

-#'  objType = "medium")

+#' AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath, objType = "medium")

 #' plotAlignmentPath(AlignObjOutput)

 #' @export

 plotAlignmentPath <- function(AlignObjOutput){

-  Alignobj <- AlignObjOutput[[1]][[1]]

-  analyte <- names(AlignObjOutput)[1]

-  s <- Alignobj@s

-  Path <- Alignobj@path[2:nrow(Alignobj@path), 2:ncol(Alignobj@path)]

-  lattice::levelplot(s, axes = TRUE, xlab = "ref index", ylab = "eXp index",

+  vec <- AlignObjOutput[[1]][,"runName"]

+  names(vec) <- rownames(AlignObjOutput[[1]])

+  pair <- names(AlignObjOutput[[2]][[1]])

+  ref <- strsplit(pair, split = "_")[[1]][1]

+  eXp <- strsplit(pair, split = "_")[[1]][2]

+  AlignObj <- AlignObjOutput[[2]][[1]][[pair]][["AlignObj"]]

+  analyte <- names(AlignObjOutput[[2]])[1]

+

+  s <- slot(AlignObj, "s")

+  Path <- slot(AlignObj, "path")

+  Path <- Path[2:nrow(Path), 2:ncol(Path)]

+  lattice::levelplot(s, axes = TRUE, xlab = vec[[ref]], ylab = vec[[eXp]],

             main = paste0("Hybrid alignment through the similarity matrix\n for ",

                           analyte), fontsize = 7) +

     latticeExtra::as.layer(lattice::levelplot(Path, col.regions = c("transparent", "green"),

@@ -30,11 +30,14 @@ AlignObj is the output from getAlignObjs fucntion. This function prepares ggplot

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

 runs <- c("hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt",

  "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt")

-AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath)

-AlignObj <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[1]]

-XICs.ref <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[2]]

-XICs.eXp <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[3]]

-refPeakLabel <- AlignObjOutput[["QFNNTDIVLLEDFQK_3"]][[4]]

+AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath)

+AlignObj <- AlignObjOutput[[2]][["4618"]][[1]][["AlignObj"]]

+XICs.ref <- AlignObjOutput[[2]][["4618"]][[1]][["ref"]]

+XICs.eXp <- AlignObjOutput[[2]][["4618"]][[1]][["eXp"]]

+refPeakLabel <- AlignObjOutput[[2]][["4618"]][[1]][["peak"]]

+\dontrun{

+getAlignedFigs(AlignObj, XICs.ref, XICs.eXp, refPeakLabel)

+}

 }

 \author{

 Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}

@@ -6,14 +6,15 @@

 AlignObjOutput is the output from getAlignObjs fucntion.}

 \usage{

 plotAlignedAnalytes(AlignObjOutput, plotType = "All",

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

+  outFile = "AlignedAnalytes.pdf", annotatePeak = FALSE,

+  saveFigs = FALSE)

 }

 \arguments{

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

+\item{AlignObjOutput}{(list) list contains fileInfo, 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{plotType}{(string) must be one of the strings "All", "onlyUnaligned" and "onlyAligned".}

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

+\item{outFile}{(string) name of the output pdf file.}

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

@@ -30,7 +31,7 @@ AlignObjOutput is the output from getAlignObjs fucntion.

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

 runs <- c("hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt",

  "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt")

-AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath)

+AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath)

 plotAlignedAnalytes(AlignObjOutput)

 }

 \author{

@@ -21,8 +21,7 @@ library(lattice)

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

 runs <- c("hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt",

  "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt")

-AlignObjOutput <- getAlignObjs(analytes = "QFNNTDIVLLEDFQK_3", runs, dataPath = dataPath,

- objType = "medium")

+AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath, objType = "medium")

 plotAlignmentPath(AlignObjOutput)

 }

 \author{

@@ -5,34 +5,29 @@

 \title{Plot extracted-ion chromatogram.}

 \usage{

 plotAnalyteXICs(analyte, run, dataPath = ".", maxFdrQuery = 1,

-  XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 9,

-  runType = "DIA_proteomics", oswMerged = TRUE,

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

-  peakAnnot = NULL, Title = NULL)

+  XICfilter = "sgolay", polyOrd = 4, kernelLen = 9,

+  runType = "DIA_proteomics", oswMerged = TRUE, 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{analyte}{(integer) an analyte is a PRECURSOR.ID from the osw file.}

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

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

+\item{dataPath}{(string) 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{XICfilter}{(string) must be either sgolay, boxcar, gaussian, loess or none.}

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

+\item{polyOrd}{(integer) order of the polynomial to be fit in the kernel.}

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

+\item{kernelLen}{(integer) number of data-points to consider in the kernel.}

 \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.}

@@ -46,9 +41,8 @@ Plot extracted-ion chromatogram.

 \examples{

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

 run <- "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt"

-plotAnalyteXICs(analyte = "QFNNTDIVLLEDFQK_3", run, dataPath = dataPath, XICfilter = "none")

-plotAnalyteXICs(analyte = "14299_QFNNTDIVLLEDFQK/3", run, dataPath = dataPath,

-XICfilter = "sgolay", analyteInGroupLabel = TRUE)

+plotAnalyteXICs(analyte = 2474L, run, dataPath = dataPath, oswMerged = TRUE, XICfilter = "none")

+plotAnalyteXICs(analyte = 2474L, run, dataPath = dataPath, oswMerged = TRUE, XICfilter = "sgolay")

 }

 \author{

 Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}

@@ -24,13 +24,13 @@ Plot Extracted-ion chromatogram group.

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

 runs <- c("hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt",

  "hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt")

-XICs <- getXICs(analytes = "QFNNTDIVLLEDFQK_3", runs = runs, dataPath = dataPath,

- XICfilter = "none")

-plotXICgroup(XICs[["hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt"]][[1]])

+XICs <- getXICs(analytes = 4618L, runs = runs, dataPath = dataPath, oswMerged = TRUE)

+plotXICgroup(XICs[["hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]])

+XICs <- smoothXICs(XICs[["hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]],

+  type = "sgolay", kernelLen = 13, polyOrd = 4)

+plotXICgroup(XICs, Title = "Precursor 4618 \\n

+ run hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt")

-XICs <- getXICs(analytes = "14299_QFNNTDIVLLEDFQK/3", runs = runs, dataPath = dataPath,

-       XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 13, analyteInGroupLabel = TRUE)

-plotXICgroup(XICs[["hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt"]][[1]])

 }

 \author{

 Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}