query_multiple {FlowSOM} | R Documentation

## query_multiple

### 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

    query_multiple(fsom, cell_types, pdf_name = "query_multiple.pdf", ...)

### Arguments

`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 `QueryStarPlot`

### Value

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

### See Also

`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)
       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")

[Package FlowSOM version 2.2.0 Index]