pigmentGate {cyanoFilter}R Documentation

gates out or assign indicators to phytoplankton cells based on the expression of the measured pigments.

Description

This function takes in a flowframe with debris removed and identifies phytoplankton cell population in the provided frame.

Usage

pigmentGate(flowfile, pig_channels, ph = 0.05)

Arguments

flowfile

flowframe after debris are removed.

pig_channels

flowcytometer channels measuring phytoplankton pigmentations.

ph

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

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

list 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'))
cyanoFilter::pigmentGate(flowfile = flowfile_logtrans,
pig_channels = c("RED.B.HLin", "YEL.B.HLin",
                    "FSC.HLin", "RED.R.HLin"),
ph = 0.06)



[Package cyanoFilter version 1.0.0 Index]