PCA plot of loadings — calcPlotPCAloadings • MetFamily

Show feature loadings on a PCA plot.

Usage

calcPlotPCAloadings(
  pcaObj,
  dataList,
  filterVec = NULL,
  pcaDimensionOne = 1,
  pcaDimensionTwo = 2,
  selectionFragmentPcaLoadingSet = NULL,
  selectionAnalysisPcaLoadingSet = NULL,
  selectionSearchPcaLoadingSet = NULL,
  xInterval = NULL,
  yInterval = NULL,
  loadingsLabels = "None",
  showLoadingsAbundance = FALSE,
  showLoadingsFeaturesAnnotated = TRUE,
  showLoadingsFeaturesUnannotated = TRUE,
  showLoadingsFeaturesSelected = TRUE,
  showLoadingsFeaturesUnselected = TRUE
)

Arguments

pcaObj: output from function calculatePCA
dataList: dataList object
filterVec: deprecated, use filterObj element in calculatePCA() instead
pcaDimensionOne: numeric PCA dimension for x axis
pcaDimensionTwo: numeric PCA dimension for y axis
selectionFragmentPcaLoadingSet: numeric vector of indices
selectionAnalysisPcaLoadingSet: numeric vector of indices
selectionSearchPcaLoadingSet: numeric vector of indices
xInterval: numeric Plot parameter
yInterval: numeric Plot parameter
loadingsLabels: boolean One of "None", "m/z / RT", "Metabolite name", or "Metabolite family"
showLoadingsAbundance: logical
showLoadingsFeaturesAnnotated: logical
showLoadingsFeaturesUnannotated: logical
showLoadingsFeaturesSelected: logical
showLoadingsFeaturesUnselected: logical

Value

a resultList object with annotation colors