PlotMarker {FlowSOM} | R Documentation

## PlotMarker

### Description

Plot comparison with other clustering

### Usage

    PlotMarker(
      fsom,
      marker,
      refMarkers = fsom$map$colsUsed,
      title = GetMarkers(fsom, marker),
      colorPalette = FlowSOM_colors,
      lim = NULL,
      ...
    )

### Arguments

`fsom` | FlowSOM object
`marker` | A vector of markers/channels to plot.
`refMarkers` | Is used to determine relative scale of the marker that will be plotted. Default are all markers used in the clustering.
`title` | A vector with custom titles for the plot. Default is the marker name.
`colorPalette` | Colorpalette to use. Can be a function or a vector.
`lim` | Limits for the scale
`...` | Additional arguments to pass to `PlotFlowSOM`, e.g. view, backgroundValues, equalNodeSize ...

### Details

Plot FlowSOM grid or tree, coloured by node values for a specific marker

### Value

A ggplot figure is returned in which every cluster is colored according to the MFI value for the specified marker

### See Also

`PlotStars`, `PlotVariable`

### Examples

    # Build FlowSOM model
    fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
    flowSOM.res <- FlowSOM(fileName,
                           compensate = TRUE, transform = TRUE, scale = FALSE,
                           colsToUse = c(9, 12, 14:18),
                           nClus = 10,
                           seed = 1)
    # Plot one marker
    PlotMarker(flowSOM.res,
               "CD19")

    PlotMarker(flowSOM.res,
               "CD19",
               colorPalette = c("grey", "red"))

    # Plot all markers
    PlotMarker(flowSOM.res,
               c(9, 12, 14:18))

    # Use specific limits if the ones from the columns used for clustering
    # are not relevant for  your marker of choice
    PlotMarker(flowSOM.res,
               "FSC-A",
                lim = c(55000, 130000))

    # Example with additional FlowSOM plotting options
    PlotMarker(flowSOM.res,
               "CD19",
               view = "grid",
               equalNodeSize = TRUE,
               backgroundValues = 1:100 == 27,
               backgroundColors = c("white", "red"))

[Package FlowSOM version 2.2.0 Index]