ProcessGatingML {FlowSOM} | R Documentation |
Reads a gatingML file using the flowUtils
library and
returns a list with a matrix containing filtering results for each specified
gate and a vector with a label for each cell
ProcessGatingML(flowFrame, gatingFile, gateIDs, cellTypes, silent = FALSE)
flowFrame |
The flowFrame to apply the gating on |
gatingFile |
The gatingML file to read |
gateIDs |
Named vector containing ids to extract from the gatingML file to use in the matrix |
cellTypes |
Cell types to use for labeling the cells. Should be a subset of the names of the gateIDs |
silent |
If FALSE, show messages of which gates are being processed |
This function returns a list in which the first element ("matrix") is a matrix containing filtering results for each specified gate and the second element ("manual") is a vector which assigns a label to each cell
# Read the flowFrame fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM") ff <- flowCore::read.FCS(fileName) ff_c <- flowCore::compensate(ff,flowCore::description(ff)$SPILL) flowCore::colnames(ff_c)[8:18] <- paste("Comp-", flowCore::colnames(ff_c)[8:18], sep="") # Specify the gating file and the gates of interest gatingFile <- system.file("extdata","manualGating.xml", package="FlowSOM") gateIDs <- c( "B cells"=8, "ab T cells"=10, "yd T cells"=15, "NK cells"=5, "NKT cells"=6) cellTypes <- c("B cells","ab T cells","yd T cells", "NK cells","NKT cells") gatingResult <- ProcessGatingML(ff_c, gatingFile, gateIDs, cellTypes) # Build a FlowSOM tree flowSOM.res <- FlowSOM(ff_c,compensate=FALSE,transform=TRUE, toTransform=8:18,colsToUse=c(9,12,14:18),nClus=10) # Plot pies indicating the percentage of cell types present in the nodes PlotPies(flowSOM.res[[1]],gatingResult$manual)