MarginEvents: the marginEvent class

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

Description

the marginEvent class

constructor for the MarginEvents class

Usage

MarginEvents(
  fullflowframe,
  reducedflowframe,
  N_margin,
  N_nonmargin,
  N_particle,
  Channel,
  y_toplot,
  cut
)

MarginEvents(
  fullflowframe,
  reducedflowframe,
  N_margin,
  N_nonmargin,
  N_particle,
  Channel,
  y_toplot,
  cut
)

Arguments

fullflowframe	same as the input flowFrame
reducedflowframe	a partial flowframe containing non-margin events
N_margin	number of margin particles measured
N_nonmargin	number of non-margine particles
N_particle	total number of particles measured
Channel	channel measuring the width of the particles
y_toplot	another channel to use in a bivariate plot
cut	the cut-off point estimated or supplied.

Value

object of class MarginEvents

Slots

fullflowframe

object of class "flowFrame" same as the input flowFrame

reducedflowframe

object of class "flowFrame" a partial flowframe containing a proportion of the measured particles

N_margin

object of class "numeric" representing the proportion of particles in each cluster

N_nonmargin

object of class "integer" representing the number of particles in each cluster

N_particle

object of class "integer" representing the labels for each cluster

Channel

object of class character representing channel measuring cell width

y_toplot

object of class character representing plot variable

cut

object of class numberic representing estimated inflection point or supplied cut-off point

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.