QueryMultiple: QueryMultiple

In SofieVG/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

QueryMultiple

Description

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).

Usage

QueryMultiple(fsom, cellTypes, plotFile = "queryMultiple.pdf", ...)

Arguments

fsom	FlowSOM object
cellTypes	Description of the cell types. Named list, with one named vector per cell type containing "high"/"low" values
plotFile	Path to a pdf file to save the plots (default is queryMultiple.pdf). If NULL, no plots will be generated
...	Additional arguments to pass to QueryStarPlot

Value

A label for every FlowSOM cluster (Unknown or one of the celltype names of the list, if selected by QueryStarPlot)

Examples

   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)
   cellTypes <- 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, cellTypes, "query_multiple.pdf")
   

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.