phytoFilter {cyanoFilter}R Documentation

gates out and assign indicators to phytoplankton cells based on the expression of measured cell complexity channels.

Description

This function takes in a flowframe with debris removed and identifies the different phytoplankton cell population based on cell pigmentation and/or complexity.

Usage

phytoFilter(
  flowfile,
  pig_channels = NULL,
  com_channels = NULL,
  ph = 0.05,
  proportion = 0.8
)

Arguments

flowfile

flowframe after debris are removed.

pig_channels

flowcytometer channels measuring cell pigments.

com_channels

flowcytometer channels measuring cell complexity.

ph

maximum peak height to be ignored. This allows ignoring of tiny peaks that could affect the gating process.

proportion

proportion of cell count to be returned.

Details

The function uses the getPeaks and deGate functions in the flowDensity package to identify peaks and identify cut-off points between these peaks.

Value

object of class PhytopFilter containing;

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)
phytoFilter(flowfile = reducedFlowframe(cells_nodebris),
              pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"),
              com_channels = c("FSC.HLin", "SSC.HLin"))




[Package cyanoFilter version 1.1.1 Index]