Merge pull request #76 from ipb-halle/feature/cleanup-and-refactor

[WIP] Feature/cleanup and refactor

DESCRIPTION

@@ -31,26 +31,36 @@ Depends:
     matrixStats,
     plotrix,
     slam,
-    plotly,
-    egg
+    plotly
+Imports:
+    egg,
+    graphics,
+    grDevices,
+    methods,
+    stats,
+    utils
 Remotes: decisionpatterns/searchable
 Suggests:
     knitr,
     testthat
 VignetteBuilder: knitr
 Maintainer: Hendrik Treutler<[email protected]>
-Description: We present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide.
-License: GPL (>= 2)
+Description: We present a novel approach for the untargeted discovery 
+  of metabolite families offering a bird's eye view of metabolic regulation 
+  in comparative metabolomics. We implemented the presented methodology 
+  in the easy-to-use web application MetFamily to enable the analysis 
+  of comprehensive metabolomics studies for all researchers worldwide.
+License: GPL (>= 2) + file LICENSE
 biocViews: Software, Visualization
 Collate:
     'Annotation.R'
     'Classifiers.R'
     'runMetFamily.R'
-    'R_packages.R'
     'FragmentMatrixFunctions.R'
     'DataProcessing.R'
     'Analysis.R'
     'TreeAlgorithms.R'
     'Plots.R'
+    'R_packages.R'
 RoxygenNote: 7.2.3
 Encoding: UTF-8

NAMESPACE

@@ -1,6 +1,28 @@
-#export(startMetFamily)
-exportPattern("^[^\\.]")
+# Generated by roxyXXXgen2: do not edit by hand
 
+## Hardcoded:
+exportPattern("^[^\\.]")
 import(egg)
+importFrom("grDevices", "as.raster", "rainbow", "rgb")
+importFrom("methods", "as")
+importFrom("graphics", "axis", "mtext", "par", "plot.new",
+           "plot.window", "points", "rasterImage", "rect", "segments",
+           "title")
+importFrom("methods", "as", "is")
+importFrom("stats", "as.dendrogram", "cor", "dendrapply", "dist",
+           "hclust", "is.leaf", "median", "na.omit", "predict", "sd")
+importFrom("utils", "flush.console", "read.table")
 
 
+## From roxygen:
+export(calcPlotDendrogram_plotly)
+export(calcPlotHeatmapLegend)
+export(castListEntries)
+export(data.numericmatrix)
+export(metaboliteFamilyVersusClass)
+export(mzClustGeneric)
+export(processMS1data)
+export(readClusterDataFromProjectFile)
+export(readProjectData)
+export(runMetFamily)
+importFrom(grDevices,colorRampPalette)

R/Annotation.R

@@ -822,6 +822,24 @@ evaluatePutativeMetaboliteFamiliesOfPrecursorSet_old <- function(dataList, precu
   return(printPutativeMetaboliteFamilies)
 }
 
+
+
+#' Title
+#'
+#' @param dataList 
+#' @param precursorSet 
+#' @param classToSpectra_class 
+#' @param properties_class 
+#' @param classifierClass 
+#' @param mappingSpectraToClassDf 
+#' @param addClassifierConsensusSpectrum 
+#'
+#' @return
+#' @export
+#' @importFrom grDevices colorRampPalette
+#' 
+#'
+#' @examples
 metaboliteFamilyVersusClass <- function(dataList, precursorSet, classToSpectra_class, properties_class, classifierClass, mappingSpectraToClassDf, addClassifierConsensusSpectrum){
   returnObj <- getSpectrumStatistics(dataList = dataList, precursorSet = precursorSet)
   masses_spec <- returnObj$fragmentMasses