PhytoFilter: gates out and 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 the different phytoplankton cell population based on cell pigmentation and/or complexity.

Usage

phytoFilter(
  flowfile,
  pig_channels = NULL,
  com_channels = NULL,
  ph = 0.05,
  proportion = 0.8
)

Arguments

flowfile	flowframe after debris are removed.
pig_channels	flowcytometer channels measuring cell pigments.
com_channels	flowcytometer channels measuring cell complexity.
ph	maximum peak height to be ignored. This allows ignoring of tiny peaks that could affect the gating process.
proportion	proportion of cell count to be returned.

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

object of class PhytopFilter containing;

• fullflowframe - flowframe containing all phytoplankton cells with added columns indicating cluster

• flowframe_proportion - a part of fullflowframe containing proportion of cell count.

• clusters_proportion - proportion of cells in each cluster

• particles_per_cluster - number of particles per cluster

• Cluster_ind - indicator for each cluster

• gated_channels - channels with multiple peaks

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")
cells_nodebris <- debrisNc(flowframe = reducedFlowframe(cells_nonmargin),
                            ch_chlorophyll = "RED.B.HLin",
                            ch_p2 = "YEL.B.HLin",
                            ph = 0.05)
phytoFilter(flowfile = reducedFlowframe(cells_nodebris),
              pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"),
              com_channels = c("FSC.HLin", "SSC.HLin"))

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