Description Usage Arguments Value See Also Examples
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
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | # 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)
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