QueryStarPlot {FlowSOM} | R Documentation

## Query a certain cell type

### Description

Identify nodes in the tree which resemble a certain profile of "high" or "low" marker expressions.

### Usage

    QueryStarPlot(fsom, query, plot = TRUE, color = "#ca0020", debug = FALSE, ...)

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST` or the first list item of `FlowSOM`
`query` | Array containing "high" or "low" for the specified column names of the FlowSOM data
`plot` | If true, a plot with a gradient of scores for the nodes is shown
`color` | Color to use for nodes with a high score in the plot
`debug` | If TRUE, some extra output will be printed
`...` | Other parameters to pass to `PlotStars`

### Value

A list, containing the ids of the selected nodes, the individual scores for all nodes and the scores for each marker for each node

### Examples

       file <- system.file("extdata", "68983.fcs", package="FlowSOM")
       # Use the wrapper function to build a flowSOM object (saved in fsom[[1]])
       # and a metaclustering (saved in fsom[[2]])
       fsom <- FlowSOM(file,compensate = TRUE, transform = TRUE,scale = TRUE,
                      colsToUse = c(9,12,14:18), nClus = 10, silent = FALSE,
                      xdim=7, ydim=7)
       query <- c("PE-Cy7-A" = "high", #CD3
                  "APC-Cy7-A" = "high", #TCRb
                  "Pacific Blue-A" = "high") #CD8
       query_res <- QueryStarPlot(UpdateNodeSize(fsom[[1]],reset=TRUE), query)

       cellTypes <- factor(rep("Unknown",49),levels=c("Unknown","CD8 T cells"))
       cellTypes[query_res$selected] <- "CD8 T cells"
       PlotStars(fsom[[1]],
                     backgroundValues=cellTypes,
                     backgroundColor=c("#FFFFFF00","#ca0020aa"))

[Package FlowSOM version 1.19.4 Index]