GetFlowJoLabels {FlowSOM} | R Documentation |
Reads a flowjo workspace file using the flowWorkspace
library
and returns a list with a matrix containing gating results and a vector with
a label for each cell from a set of specified gates
GetFlowJoLabels( files, wsp_file, group = "All Samples", cell_types = NULL, get_data = FALSE, ... )
files |
The fcs files of interest |
wsp_file |
The FlowJo wsp file to read |
group |
The FlowJo group to parse. Default "All Samples". |
cell_types |
Cell types to use for final labeling the cells. Should correspond with a subset of the gate names in FlowJo. |
get_data |
If true, flowframes are returned as well. |
... |
Extra arguments to pass to CytoML::flowjo_to_gatingset |
This function returns a list, which for every file contains 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 one label to each cell. If only one file is given, only one list is returned instead of a list of lists.
# Identify the files fcs_file <- system.file("extdata", "68983.fcs", package = "FlowSOM") wsp_file <- system.file("extdata", "gating.wsp", package = "FlowSOM") # Specify the cell types of interest for assigning one label per cell cell_types <- c("B cells", "gd T cells", "CD4 T cells", "CD8 T cells", "NK cells","NK T cells") # Parse the FlowJo workspace gatingResult <- GetFlowJoLabels(fcs_file, wsp_file, cell_types = cell_types, get_data = TRUE) # Check the number of cells assigned to each gate colSums(gatingResult$matrix) # Build a FlowSOM tree flowSOM.res <- FlowSOM(gatingResult$flowFrame, colsToUse = c(9,12,14:18), nClus = 10, seed = 1) # Plot pies indicating the percentage of cell types present in the nodes PlotPies(flowSOM.res$FlowSOM, gatingResult$manual, backgroundValues = flowSOM.res$metaclustering)