clusterExtract {cyanoFilter} | R Documentation |
extract clusters based on supplied cluster indicator
clusterExtract(flowfile, cluster_var = "Clusters", cluster_val = NULL)
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. |
flowFrame containing the clusters
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)