query_multiple {FlowSOM} | R Documentation |
Function which takes a named list of multiple cell types, where every item is a named vector with values "high"/"low" and the names correspond to the markers or channels (e.g. as generated by parse_markertable).
query_multiple(fsom, cell_types, pdf_name = "query_multiple.pdf", ...)
fsom |
FlowSOM object |
cell_types |
Description of the cell types. Named list, with one named vector per cell type containing "high"/"low" values |
pdf_name |
Path to a pdf file to save figures |
... |
Additional arguments to pass to |
A label for every FlowSOM cluster (Unknown or one of the celltype names of the list, if selected by QueryStarPlot)
file <- system.file("extdata", "68983.fcs", package="FlowSOM") ff <- flowCore::read.FCS(file) # Use the wrapper function to build a flowSOM object (saved in flowSOM.res) # and a metaclustering (saved in flowSOM.res[["metaclustering"]]) flowSOM.res <- FlowSOM(ff,compensate = TRUE, transform = TRUE,scale = TRUE, colsToUse = c(9,12,14:18), nClus = 10, silent = FALSE, xdim=7, ydim=7) cell_types <- list("CD8 T cells" = c("PE-Cy7-A" = "high", "APC-Cy7-A" = "high", "Pacific Blue-A" = "high"), "B cells" = c("PE-Cy5-A" = "high"), "NK cells" = c("PE-A" = "high", "PE-Cy7-A" = "low", "APC-Cy7-A" = "low")) query_res <- QueryMultiple(flowSOM.res, cell_types, "query_multiple.pdf")