pigmentGate {cyanoFilter} | R Documentation |
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)
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. |
The function uses the getPeaks
and
deGate
functions in the
flowDensity package to identify peaks and identify cut-off
points between these peaks.
list containing;
full_flowframe - flowframe containing only phytoplankton cells
phy_ind - indicator for phytoplankton clusters found
gated_channels - pigment channels with more than one peak
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)