clusterExtract: extract clusters based on supplied cluster indicator

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

Description

extract clusters based on supplied cluster indicator

Usage

clusterExtract(flowfile, cluster_var = "Clusters", cluster_val = NULL)

Arguments

flowfile	flowframe containing cluster indicators as well
cluster_var	column name in expression matrix containing the cluter indicators, cannot be NULL.
cluster_val	cluster number, cannot be NULL.

Value

flowFrame containing the clusters

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 <- cyanoFilter::lnTrans(x = flowfile_noneg, 
                                         c('SSC.W', 'TIME'))
cells_nonmargin <- cellMargin(flowframe = flowfile_logtrans, 
                              Channel = 'SSC.W',
           type = 'estimate', y_toplot = "FSC.HLin")
fin <- phytoFilter(flowfile = reducedFlowframe(cells_nonmargin),
              pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"),
              com_channels = c("FSC.HLin", "SSC.HLin"))

clusterExtract(flowfile = reducedFlowframe(fin),
    cluster_var = "Clusters",
    cluster_val = 1)

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