reducedFlowframe-PhytopFilter-method: accesor method for reduced flowframe(PhytoFilter class)

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

Description

accesor method for reduced flowframe(PhytoFilter class)

Usage

## S4 method for signature 'PhytopFilter'
reducedFlowframe(x)

Arguments

x	an object of class PhytoFilter

Value

reduced flowFrame method for PhytoFilter #' @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) phy1 <- phytoFilter(flowfile = reducedFlowframe(cells_nodebris), pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"), com_channels = c("FSC.HLin", "SSC.HLin")) reducedFlowframe(phy1)

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