cellmargin: Removes or assign indicators to margin events.

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

Description

The function identifies margin events, i.e. cells that are too large for the flow cytometer to measure.

Usage

cellMargin(
  flowframe,
  Channel = "SSC.W",
  type = c("manual", "estimate"),
  cut = NULL,
  y_toplot = "FSC,HLin"
)

Arguments

flowframe	Flowframe containing margin events to be filtered out
Channel	The channel on which margin events are. Defaults to SSC.W (side scatter width)
type	The method to be used in gating out the margin cells. Can either be 'manual' where user supplies a cut off point on the channel, 1 = not margin 0 = margin
cut	sould not be NULL if type = 'manual'
y_toplot	channel on y-axis of plot with Channel used to gate out margin events

Details

Users can either supply a cut-off point along the channel describing particle width or allow the function to estimate the cut-off point using the deGate function from the flowDensity package. A plot of channel against "FSC.HLin" is provided with a vertical line showing the cut-off point separating margin events from other cells.

Value

an object of class MarginEvents class containing slots;

• reducedflowframe - flowframe without margin events

• fullflowframe - flowframe with an Margin.Indicator added as an extra column added to the expression matrix to indicate which particles are margin events. 1 = not margin event, 0 = margin event

• N_margin - number of margin events recorded

• N_cell - numner of non-margin events

• N_particle - is the number of particles in total, i.e. N_cell + N_margin

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 <- lnTrans(x = flowfile_noneg, c('SSC.W', 'TIME'))
cellMargin(flowframe = flowfile_logtrans, Channel = 'SSC.W',
           type = 'estimate', y_toplot = "FSC.HLin")

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