clusterExtractp {cyanoFilter} | R Documentation |
takes a flowframe, name of cluster column and extracts part of flowframe that makes up proportion.
clusterExtractp(flowfile, cluster_var = "Clusters", proportion = 1)
flowfile |
flowframe after debris are removed. |
cluster_var |
column name in expression matrix containing the cluter indicators |
proportion |
value between 0 and 1 indicating percentage of the total particles wanted |
a list containing
particles_per_cluster
clusters_proportion
flowfile_proportion
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 <- cyanoFilter::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")) clusterExtractp(flowfile = reducedFlowframe(fin), cluster_var = "Clusters", proportion = 0.80)