PhytopFilter: the phytofilter class

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

Description

the phytofilter class

constructor for the PhytoFilter class

Usage

PhytopFilter(
  fullflowframe,
  flowframe_proportion,
  clusters_proportion,
  particles_per_cluster,
  Cluster_ind,
  gated_channels,
  channels
)

PhytopFilter(
  fullflowframe,
  flowframe_proportion,
  clusters_proportion,
  particles_per_cluster,
  Cluster_ind,
  gated_channels,
  channels
)

Arguments

fullflowframe	same as the input flowFrame
flowframe_proportion	a partial flowframe containing containing a proportion of the measured particles
clusters_proportion	number of margin particles measured
particles_per_cluster	number of particles in each cluster
Cluster_ind	labels for each cluster
gated_channels	channels used for gating
channels	all channels supplied

Value

object of class PhytoFilter

Slots

fullflowframe

object of class "flowFrame" same as the input flowFrame

flowframe_proportion

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

clusters_proportion

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

particles_per_cluster

object of class "data.frame" representing the number of particles in each cluster

Cluster_ind

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

gated_channels

object of class "character" representing the names of channels with multiple peaks

channels

object of class "character" representing the names of the channels

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")
           
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.