debrisNc: gates out or assign indicators to debris particle based on...

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

Description

The function takes in a flowframe and identifies debris contained in the provided flowframe.

Usage

debrisNc(flowframe, ch_chlorophyll, ch_p2, ph = 0.09, n_sd = 2)

Arguments

flowframe	flowframe with debris and other cells.
ch_chlorophyll	first flowcytometer channel that can be used to separate debris from the rest, e.g. "RED.B.HLin".
ch_p2	second flowcytometer channel use for plotting from the rest, e.g. "YEL.B.HLin"
ph	the minimum peak height that should be considered. This aids the removal of tiny peaks. Defaults to 0.1
n_sd	number of standard deviations away from peak should be considered to filter out debris

Details

The function uses the getPeaks and deGate functions in the flowDensity package to identify peaks in ch_chlorophyll, and identify cut-off points #between these peaks. A plot of both channels supplied with horizontal line separating debris from other cell populations is also returned.

Value

list containing;

• syn - flowframe containing non-debris particles

• deb_pos - position of particles that are debris

• syn_pos - position of particles that are not debris

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")
debrisNc(flowframe = reducedFlowframe(cells_nonmargin), 
          ch_chlorophyll = "RED.B.HLin",
          ch_p2 = "YEL.B.HLin",
          ph = 0.05)

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