This function takes in a flowframe with debris removed and identifies phytoplankton cell population in the provided frame.
pigmentGate(flowfile, pig_channels, ph = 0.05)
flowframe after debris are removed.
flowcytometer channels measuring phytoplankton pigmentations.
maximum peak height to be ignored. This allows ignoring of tiny peaks that could affect the gating process.
The function uses the
deGate functions in the
flowDensity package to identify peaks and identify cut-off
points between these peaks.
full_flowframe - flowframe containing only phytoplankton cells
phy_ind - indicator for phytoplankton clusters found
gated_channels - pigment channels with more than one peak
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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)
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