pigmentGate: gates out or assign indicators to phytoplankton cells based...

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

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;

• full_flowframe - flowframe containing only phytoplankton cells

• phy_ind - indicator for phytoplankton clusters found

• gated_channels - pigment channels with more than one peak

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)

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