accTest: 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

accTest(
  fs,
  sfts = c("phytoFilter", "flowClust", "cytometree"),
  channels,
  nrun = 10000,
  ...
)

Arguments

fs	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
nrun	number of times the resampling should be done
...	extra options to be parsed to the gating function

Value

a named list containing the following objects;

• depth - the multivariate-depth (median) of each flowFrame in the flowset supplied

• accuracy - computed accuracy based on resampling after joining the flowFrames together.

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)
              )

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