PhytopFilter {cyanoFilter} | R Documentation |
the phytofilter class
constructor for the PhytoFilter class
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 )
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 |
object of class PhytoFilter
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
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")