QueryStarPlot {FlowSOM} | R Documentation

## QueryStarPlot

### Description

Query a certain cell type

### Usage

    QueryStarPlot(
      fsom,
      query,
      plot = TRUE,
      colorPalette = FlowSOM_colors,
      backgroundColors = "#CA0020",
      ...
    )

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`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.
`colorPalette` | ColorPalette to be used for colors for "stars", "pies" or "marker". Can be either a function or an array specifying colors.
`backgroundColors` | Color to use for nodes with a high score in the plot. Default is red.
`...` | Additional arguments to pass to `PlotFlowSOM`

### Details

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

### 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

### See Also

`PlotStars`, `PlotVariable`, `PlotFlowSOM`, `PlotLabels`, `PlotNumbers`, `PlotMarker`, `PlotPies`, `PlotSD`

### Examples

       file <- system.file("extdata", "68983.fcs", package="FlowSOM")
       flowSOM.res <- FlowSOM(file, compensate = TRUE, transform = TRUE,
                      scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10,
                      silent = FALSE, xdim = 7, ydim = 7)
       query <- c("CD3" = "high", #CD3
                  "CD4" = "low", #TCRb
                  "CD8" = "high") #CD8
       query_res <- QueryStarPlot(flowSOM.res, query, equalNodeSize = TRUE)

       cellTypes <- factor(rep("Unlabeled", 49),
                           levels = c("Unlabeled", "CD8 T cells"))
       cellTypes[query_res$selected] <- "CD8 T cells"
       PlotStars(flowSOM.res,
                 backgroundValues = cellTypes,
                 backgroundColors = c("#FFFFFF00", "#ca0020aa"))

[Package FlowSOM version 2.2.0 Index]