gateFunc: tests the accuracy of several automated gating functions on...

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

Description

This function gates all flowFrames in the supplied flowSet to attach cluster labels. Then it mixes up the flowSet into one giant flowFrame and re-gates this to attach another label. These labels are used to examine if the gating algorithms can reproduce the earlier clusters before the mixing.

Usage

gateFunc(
  flowfile,
  sfts = c("phytoFilter", "flowClust", "cytometree"),
  channels,
  funargs_list
)

Arguments

flowfile	flowSet with each flowFrame being a phytoplankton monoculture FCM experiment
sfts	character vector of gating function to test.
channels	channels to be used for gating
funargs_list	additional options for the chosen gating function

Value

a flowFrame with cluster indicator generated by the software used added to the expression matrix.

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 specification
gateFunc(flowfile = reducedFlowframe(cells_nodebris),
              channels = c("RED.B.HLin", "YEL.B.HLin", 
              "RED.R.HLin", "FSC.HLin", "SSC.HLin"),
              sfts = "phytoFilter", 
              list(ph = 0.1, proportion = 0.90)
              )
#flowClust specification
gateFunc(flowfile = reducedFlowframe(cells_nodebris),
              channels = c("RED.B.HLin", "YEL.B.HLin", 
              "RED.R.HLin", "FSC.HLin", "SSC.HLin"),
              sfts = "flowClust", 
              list(K = 1:4, B = 100)
              )
#cytometree specification
gateFunc(flowfile = reducedFlowframe(cells_nodebris),
              channels = c("RED.B.HLin", "YEL.B.HLin", 
              "RED.R.HLin", "FSC.HLin", "SSC.HLin"),
              sfts = "cytometree", 
              list(minleaf = 1, t = 0.10)
              )

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