PlotFlowSOM {FlowSOM} | R Documentation

## PlotFlowSOM

### Description

Base layer to plot a FlowSOM result

### Usage

    PlotFlowSOM(
      fsom,
      view = "MST",
      nodeSizes = fsom$map$pctgs,
      maxNodeSize = 1,
      refNodeSize = max(nodeSizes),
      equalNodeSize = FALSE,
      backgroundValues = NULL,
      backgroundColors = NULL,
      backgroundLim = NULL,
      title = NULL
    )

### Arguments

`fsom` | FlowSOM object, as created by `FlowSOM`
`view` | Preferred view, options: "MST", "grid" or "matrix" with a matrix/dataframe consisting of coordinates given in coords. Default = "MST"
`nodeSizes` | A vector containing nodesizes. These will automatically be scaled between 0 and maxNodeSize and transformed with a sqrt. Default = fsom$MST$sizes
`maxNodeSize` | Determines the maximum nodesize. Default is 1.
`refNodeSize` | Reference for nodesize against which the nodeSizes will be scaled. Default = max(nodeSizes)
`equalNodeSize` | If `TRUE`, the nodes will be equal to maxNodeSize. If `FALSE` (default), the nodes will be scaled to the number of cells in each cluster
`backgroundValues` | Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering)
`backgroundColors` | Colorpalette to be used for the background coloring. Can be either a function or an array specifying colors.
`backgroundLim` | Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.
`title` | Title of the plot

### Details

Base layer of the FlowSOM plot, where you can choose layout (MST, grid or coordinates of your own choosing), background colors and node size. Can then be extended by e.g. `AddStars`, `AddLabels`, `AddPies`, ...

### Value

A ggplot object with the base layer of a FlowSOM plot

### See Also

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

### Examples

    # Locate file on file system
    fcs_file <- system.file("extdata", "68983.fcs", package = "FlowSOM")

    # Build FlowSOM model
    flowSOM.res <- FlowSOM(fcs_file,
                           scale = TRUE,
                           compensate = TRUE,
                           transform = TRUE,
                           toTransform = 8:18,
                           colsToUse = c(9, 12, 14:18),
                           nClus = 10,
                           seed = 1)

    # Plot with background coloring
    PlotFlowSOM(flowSOM.res,
                backgroundValues = flowSOM.res$metaclustering)

    # Own layout
    mfis <- GetClusterMFIs(flowSOM.res)[,GetChannels(flowSOM.res, c("CD3", "CD4"))]
    PlotFlowSOM(flowSOM.res,
                view = mfis,
                maxNodeSize = 0.1,
                backgroundValues = flowSOM.res$metaclustering)

    # Adapted node sizes
    PlotFlowSOM(flowSOM.res,
                  nodeSizes = 1:100,
                  view = "grid")

[Package FlowSOM version 2.2.0 Index]