R/smallMoleculeSpectraFunctions.R

In chasemc/tempRepo: Protein and small molecule analysis of bacteria by MALDI-TOF MS

# tempRepo::subtractMatrixBlank(sampleIds = labels(selectedSmallMolPeakList()), 
#                               peakList = selectedSmallMolPeakList(),
#                               binTolerance = 0.002)




#' 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 peakPercentPresence 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"
#' @export
#'
getSmallMolSpectra <- function(pool,
                               sampleIDs = NULL,
                               dendrogram,
                               brushInputs,
                               matrixIDs = NULL,
                               peakPercentPresence,
                               lowerMassCutoff,
                               upperMassCutoff, 
                               minSNR){
  
  

  checkedPool <- pool::poolCheckout(pool)
  
  
  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 <- tempRepo::labelsFromBrushedDendrogram(dendrogram = dendrogram,
                                                         #    dendrogramShortLabels = dendrogram,
                                                         brushYmin = brushInputs()$ymin,
                                                         brushYmax = brushInputs()$ymax)
    }
  } else {
    
    # retrieve all Strain_IDs in db that have small molecule spectra
    sampleIDs <- DBI::dbGetQuery(checkedPool, glue::glue("SELECT DISTINCT Strain_ID
                                      FROM IndividualSpectra 
                                      WHERE maxMass < 6000"))
    sampleIDs <- as.vector(sampleIDs)[,1]
  }
  
}
  
  samples <- lapply(sampleIDs, 
                    function(sampleIDs){ 
                      tempRepo::collapseReplicates(checkedPool = checkedPool,
                                                   sampleIDs = sampleIDs,
                                                   peakPercentPresence = peakPercentPresence,
                                                   lowerMassCutoff = lowerMassCutoff,
                                                   upperMassCutoff = upperMassCutoff,  
                                                   minSNR = minSNR, 
                                                   tolerance = 0.002,
                                                   protein = FALSE)
                      
                    })
  
  
  
  
  
  
  
  
  
  # Return pool
  pool::poolReturn(checkedPool)
  
  return(list(maldiQuantPeaks = samples,
              sampleIDs = sampleIDs))
  
}