phytoFilter {cyanoFilter} | R Documentation |
This function takes in a flowframe with debris removed and identifies the different phytoplankton cell population based on cell pigmentation and/or complexity.
phytoFilter( flowfile, pig_channels = NULL, com_channels = NULL, ph = 0.05, proportion = 0.8 )
flowfile |
flowframe after debris are removed. |
pig_channels |
flowcytometer channels measuring cell pigments. |
com_channels |
flowcytometer channels measuring cell complexity. |
ph |
maximum peak height to be ignored. This allows ignoring of tiny peaks that could affect the gating process. |
proportion |
proportion of cell count to be returned. |
The function uses the getPeaks
and
deGate
functions in the
flowDensity package to
identify peaks and identify cut-off points between these peaks.
object of class PhytopFilter containing;
fullflowframe - flowframe containing all phytoplankton cells with added columns indicating cluster
flowframe_proportion - a part of fullflowframe containing proportion of cell count.
clusters_proportion - proportion of cells in each cluster
particles_per_cluster - number of particles per cluster
Cluster_ind - indicator for each cluster
gated_channels - channels with multiple peaks
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") cells_nodebris <- debrisNc(flowframe = reducedFlowframe(cells_nonmargin), ch_chlorophyll = "RED.B.HLin", ch_p2 = "YEL.B.HLin", ph = 0.05) phytoFilter(flowfile = reducedFlowframe(cells_nodebris), pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"), com_channels = c("FSC.HLin", "SSC.HLin"))