R/fct_getSmallPeaksFromBrush.R

In chasemc/IDBac_App: MALDI-TOF MS Protien and Small Molecule Analysis

#' Retrieve small molecule and matrix peak lists and make consensus peak lists
#'
#' @param pool pool
#' @param sampleIDs character vector of IDs (currently not used)
#' @param dendrogram protein dendrogram that was brushed 
#' @param matrixIDs sampleID that will be used as a matrix
#' @param minFrequency peaks whose frequency of occurence in replicates below this are dropped
#' @param lowerMassCutoff lower mass to retain
#' @param upperMassCutoff upper mass to retain
#' @param minSNR minimum SNR a peak must have to be retained
#' @param brushInputs brusked dendrogram outputs
#'
#' @return a list containg two lists of MALDIquant peak objects "samplePeaks" and "matrixPeaks"
.getSmallPeaksFromBrush <- function(pool,
                                    sampleIDs = NULL,
                                    dendrogram,
                                    brushInputs,
                                    matrixIDs = NULL,
                                    minFrequency,
                                    lowerMassCutoff,
                                    upperMassCutoff, 
                                    minSNR){
  
  
  #TODO split the brush out into own function
  
  if (is.null(sampleIDs)) {
    
    
    if (!is.null(dendrogram)) {  
      
      # If there is a protein dendrogram but a user hasn't brushed:
      if (is.null(brushInputs()$ymin)) { 
        
        # Don't ovrwhelm the browser by displaying everthing when page loads
        if (length(labels(dendrogram)) >= 25) {
          # If more than 25 strains present, only display 10 to start, otherwise display all
          # Get random 10 strain IDs from dendrogram
          sampleIDs <- labels(dendrogram)[1:sample.int(10, 1)]
        } else {
          sampleIDs <- labels(dendrogram)
        }
      } else {
        # Get the labels of the brushed dendrogram
        sampleIDs <- labelsFromBrushedDendrogram(dendrogram = dendrogram,
                                                 brushYmin = brushInputs()$ymin,
                                                 brushYmax = brushInputs()$ymax)
      }
    } else {
      # All mall moleculesamples
      sampleIDs <- NULL
    }
    
  }
  
  idbac_get_peaks(pool = pool,
                  sampleIDs = sampleIDs,
                  minFrequency = minFrequency,
                  lowerMassCutoff = lowerMassCutoff,
                  upperMassCutoff = upperMassCutoff,  
                  minSNR = minSNR, 
                  tolerance = 0.002,
                  type = "small",
                  mergeReplicates = TRUE)
  
  
}