PlotVariable: PlotVariable

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

PlotVariable

Description

Plot a variable for all nodes

Usage

PlotVariable(
  fsom,
  variable,
  variableName = "",
  colorPalette = FlowSOM_colors,
  lim = NULL,
  ...
)

Arguments

fsom	FlowSOM object
variable	A vector containing a value for every cluster
variableName	Label to show on the legend
colorPalette	Color palette 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, colored by node values given in variable

See Also

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

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 some random values
rand <- runif(flowSOM.res$map$nNodes)
PlotVariable(flowSOM.res, 
             variable = rand,
             variableName = "Random")
             
PlotVariable(flowSOM.res, 
             variable = flowSOM.res$metaclustering,
             variableName = "Metaclustering") %>% 
  AddLabels(labels = flowSOM.res$metaclustering)             
   

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.