celldebris_nc: gates out or assign indicators to Synechococcus cyanobacteria...

In cyanoFilter: Cyanobacteria Population Identification for Flow Cytometry

Description

This is a top-level function that calls other functions to identify cell population of interest.

Usage

celldebris_nc(flowframe, channel1 = "RED.B.HLin",
  channel2 = "YEL.B.HLin", interest = c("bottom-right", "top-right",
  "both-right"), to_retain = c("refined", "potential"))

Arguments

flowframe	flowframe with debris and Synechococcus cells.
channel1	first flowcytometer channel that can be used to separate cyanobacteria cells from the rest, e.g. "RED.B.HLin".
channel2	second flowcytometer channel that can be used to separate cyanobacteria cells from the rest, e.g. "YEL.B.HLin"
interest	a string indicating poistion of population of interest to be gated, can be "bottom-right", "top-right" or "both-right".
to_retain	should potential candidates be retained or further gating be applied to filter out only certain cyano cells.

Details

The indicators assigned to the "BS4BS5.Indicator" column in the full flowframe depends on the interest supplied. For interest="bottom-right" or interest="top-right"; 0 = Debris, 1 = BS4/BS5, 2 = not-identified while for interest="Both", 0 = Debris, 1 = Syn-1, 2 = Syn-2, 3 = not-identified. This function calls the debris_nc or debris_inc function to identify debris and afterwards call the bs4_nc and/or bs5_nc depending on the interest supplied.

Value

list containing;

• fullframe - full flowframe with indicator for debris, BS4/BS5 or both.

• reducedframe - flowframe with onlySynechococcus cyanobacteria.

• Cell_count - a vector containing number of Synechococcus cyanobacteria cells. Might be a single value or vector of two values depending on interest.

• Debris_count - number of debris particles.

See Also

celldebris_emclustering

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) #FCS file contains only one data object
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(flow.frame = flowfile_logtrans, Channel = 'SSC.W',
           type = 'estimate', y_toplot = "FSC.HLin")
celldebris_nc(flowframe = cells_nonmargin$reducedframe, channel1 = "RED.B.HLin",
              channel2 = "YEL.B.HLin",
              interest = "bottom-right", to_retain = "refined")

cyanoFilter documentation built on Jan. 9, 2020, 5:08 p.m.