R/newFlowframe.R

In fomotis/cyanoFilter: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

#' takes a flowframe, a group indicator and formulates another flowframe with 
#' group indicator as part of the
#' expression matrix of the new flowframe.
#'
#' @param flowfile flowframe after debris are removed.
#' @param group cluster group to be added to the expression matrix
#' @param togate channel detected to have more than one peak
#' @return flowframe with indicators for particle cluster
#' 
#' @examples
#' flowfile_path <- system.file("extdata", "B4_18_1.fcs", 
#'                   package = "cyanoFilter",
#'               mustWork = TRUE)
#' flowfile <- flowCore::read.FCS(flowfile_path, alter.names = TRUE,
#'                                transformation = FALSE, emptyValue = FALSE,
#'                                dataset = 1) 
#' flowfile_nona <- cyanoFilter::noNA(x = flowfile)
#' flowfile_noneg <- cyanoFilter::noNeg(x = flowfile_nona)
#' flowfile_logtrans <- cyanoFilter::lnTrans(x = flowfile_noneg, 
#' c('SSC.W', 'TIME'))
#' oneDgate(flowfile, 'RED.B.HLin')
#' 
#' @export newFlowframe

newFlowframe <- function(flowfile, group = NULL, togate = NULL) {
  
  
  if(methods::is(flowfile, "list")) {
    
    mats <- do.call(rbind, lapply(flowfile, exprs))
    ddata <- pData(flowCore::parameters(flowfile[[1]]))
    dvarMetadata <- flowCore::varMetadata(flowCore::parameters(flowfile[[1]]))
    ddimnames <- dimLabels(flowCore::parameters(flowfile[[1]]))
    describe <- flowCore::keyword(flowfile[[1]])
    
  } else if(methods::is(flowfile, "flowSet")) {
    
    mats <- do.call(rbind, fsApply(flowfile, exprs))
    ddata <- pData(flowCore::parameters(flowfile[[1]]))
    dvarMetadata <- flowCore::varMetadata(flowCore::parameters(flowfile[[1]]))
    ddimnames <- dimLabels(flowCore::parameters(flowfile[[1]]))
    describe <- flowCore::keyword(flowfile[[1]])
    
  } else if(methods::is(flowfile, "flowFrame")) {
    
    if(!is.null(togate)) {
      
      ddata <- data.frame(name = paste(togate, "Cluster", sep = "_"),
                          desc = paste("Cluster Group for", togate),
                          range = max(group) - min(group),
                          minRange = range(group)[1],
                          maxRange = range(group)[2]
      )
      
    } else {
      
      ddata <- data.frame(name = "Clusters",
                          desc = paste("Detected Cluster groups"),
                          range = max(group) - min(group),
                          minRange = range(group)[1],
                          maxRange = range(group)[2]
      )
      
    }
    
    pd <- pData(flowCore::parameters(flowfile))
    ddata <- rbind(pd, ddata)
    row.names(ddata) <- c(row.names(pd),
                          paste("$P", 
                                length(row.names(pd))+1,
                                sep = ""))
    #flowframe with indicator added for each cluster
    mats <- as.matrix(cbind(flowCore::exprs(flowfile), group))
    # giving a name to the newly added column to the expression matrix
    colnames(mats) <- ddata$name
    dvarMetadata <- flowCore::varMetadata(flowCore::parameters(flowfile))
    ddimnames <- dimLabels(flowCore::parameters(flowfile))
    describe <- flowCore::keyword(flowfile)
    
    
  } else stop("invalid object supplied")


  

  
  paraa <- Biobase::AnnotatedDataFrame(data = ddata, 
                                       varMetadata = dvarMetadata,
                                       dimLabels = ddimnames
                                      )
  


  # full flow frame with indicator for particly type
  fflowframe <- flowCore::flowFrame(exprs = mats, 
                                    parameters = paraa,
                                    description = describe
                                    )
  return(fflowframe)
}