PlotStars {FlowSOM}R Documentation

PlotStars

Description

Plot star charts

Usage

PlotStars(
  fsom,
  markers = fsom$map$colsUsed,
  colorPalette = FlowSOM_colors,
  list_insteadof_ggarrange = FALSE,
  ...
)

Arguments

fsom

FlowSOM object, as generated by BuildMST

markers

Markers to plot (will be parsed by GetChannels)

colorPalette

ColorPalette to use

list_insteadof_ggarrange

If FALSE (default), the plot and the legend are combined by ggarrange. If TRUE, the seperate elements are returned in a list, to allow further customization.

...

Additional arguments to pass to PlotFlowSOM

Details

Plot FlowSOM grid or tree, where each node is represented by a star chart indicating median marker values

Value

Nothing is returned. A plot is drawn in which each node is represented by a star chart indicating the median fluorescence intensities. Resets the layout back to 1 plot at the end.

See Also

PlotMarker, PlotVariable, PlotFlowSOM, PlotLabels, PlotNumbers, PlotPies, QueryStarPlot, PlotSD

Examples

# Read from file, build self-organizing map and minimal spanning tree
fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
flowSOM.res <- FlowSOM(fileName, compensate = TRUE, transform = TRUE,
                       scale = TRUE, colsToUse = c(9, 12, 14:18))

# Plot stars indicating the MFI of the cells present in the nodes
PlotStars(flowSOM.res)


[Package FlowSOM version 2.0.0 Index]