QueryMultiple {FlowSOM} | R Documentation

## 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")

[Package FlowSOM version 2.2.0 Index]