PlotStars: PlotStars

In SofieVG/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

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	Color palette to use
list_insteadof_ggarrange	If FALSE (default), the plot and the legend are combined by ggarrange. If TRUE, the separate 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, backgroundValues = flowSOM.res$metaclustering)

newLayout <- igraph::layout_with_fr(flowSOM.res[["MST"]][["graph"]])
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering, 
          view = newLayout)
          
PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering, 
          view = "grid")

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.