summaries-PhytopFilter-method: takes a flowframes, a vector of channels, cluster indicator...

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

Description

takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster

Usage

## S4 method for signature 'PhytopFilter'
summaries(
  object,
  channels = NULL,
  cluster_var = "Clusters",
  summary = c("mean", "median", "cov", "n")
)

Arguments

object	An object of class cyanoFilter to be summarised.
channels	channels whose summaries are to be computed
cluster_var	column name in expression matrix containing the cluter indicators
summary	summary statistic of interest. Only mean and variance-covariance matrix supported at the moment.

Value

list containing computed summaires

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'))
cells_nonmargin <- cellMargin(flowframe = flowfile_logtrans, 
Channel = 'SSC.W',
           type = 'estimate', y_toplot = "FSC.HLin")
cells_nodebris <- debrisNc(flowframe = reducedFlowframe(cells_nonmargin),
                           ch_chlorophyll = "RED.B.HLin",
                            ch_p2 = "YEL.B.HLin",
                            ph = 0.05)
fin <- phytoFilter(flowfile = reducedFlowframe(cells_nodebris),
              pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"),
              com_channels = c("FSC.HLin", "SSC.HLin"))

summaries(object = fin,
        channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"),
        cluster_var = "Clusters",
        summary = 'mean')

fomotis/cyanoFilter documentation built on Aug. 1, 2021, 10:58 p.m.