Move stringr to imports

DESCRIPTION

@@ -28,7 +28,6 @@ Depends:
     gdata,
     searchable, 
     tools,
-    stringr,
     matrixStats,
     plotrix,
     slam,
@@ -43,6 +42,7 @@ Imports:
     stats,
     utils,
     S4Vectors, 
+    stringr,
     SummarizedExperiment,
     openxlsx2
 Remotes: 

NAMESPACE

@@ -40,3 +40,4 @@ importFrom("SummarizedExperiment","rowData","rowData<-")
 importFrom(SummarizedExperiment,assay)
 
 importFrom("plotly", "plot_ly", "add_trace", "layout")
+importFrom("stringr", "str_squish", "str_split")

R/DataProcessing.R

@@ -96,6 +96,7 @@ readClusterDataFromProjectFile <- function(file, progress = FALSE)
 #' 
 #' @seealso [processMS1data]
 #' @export
+#' @importFrom stringr str_split
 #'
 #' @examples
 readProjectData <- function(fileLines, progress = FALSE)

R/FragmentMatrixFunctions.R

@@ -824,6 +824,22 @@ parseMSP_chunk <- function(fileLines,
   return(returnObj)
 }
 
+
+#' parseMSP_attributes
+#'
+#' @param fileSpectra 
+#' @param progress 
+#' @param flexiblePeakList 
+#' @param multiplePeaksPerLine 
+#' @param includeIDasRecordSeparator 
+#' @param includeNAMEasRecordSeparator 
+#' @param includeTITLEasRecordSeparator 
+#' @param returnEmptySpectra 
+#'
+#' @returns
+#' @importFrom stringr str_split
+#'
+#' @examples
 parseMSP_attributes <- function(fileSpectra, progress = FALSE, flexiblePeakList = FALSE, multiplePeaksPerLine = FALSE, includeIDasRecordSeparator=TRUE, includeNAMEasRecordSeparator=TRUE, includeTITLEasRecordSeparator=TRUE, returnEmptySpectra = FALSE){
   fileLines <- readLines(con = fileSpectra)
 

R/Plots.R

@@ -2346,6 +2346,30 @@ calcPlotPCAscores <- function(pcaObj, dataList, filterObj,
   }
 }
 
+#' calcPlotPCAloadings
+#'
+#' @param pcaObj 
+#' @param dataList 
+#' @param filter 
+#' @param pcaDimensionOne 
+#' @param pcaDimensionTwo 
+#' @param selectionFragmentPcaLoadingSet 
+#' @param selectionAnalysisPcaLoadingSet 
+#' @param selectionSearchPcaLoadingSet 
+#' @param xInterval 
+#' @param yInterval 
+#' @param loadingsLabels 
+#' @param showLoadingsAbundance 
+#' @param showLoadingsFeaturesAnnotated 
+#' @param showLoadingsFeaturesUnannotated 
+#' @param showLoadingsFeaturesSelected 
+#' @param showLoadingsFeaturesUnselected 
+#'
+#' @returns
+#' @export
+#' @importFrom stringr str_squish
+#'
+#' @examples
 calcPlotPCAloadings <- function(
   pcaObj, dataList, filter, 
   pcaDimensionOne, pcaDimensionTwo,