FlowSOM (version 1.4.0)

PlotVariable: Plot a variable for all nodes

Description

Plot FlowSOM grid or tree, coloured by node values given in variable

Usage

PlotVariable(fsom, variable, view = "MST", main = NULL, colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")), symmetric = FALSE)

Arguments

fsom

FlowSOM object, as generated by BuildMST

variable

Vector containing a value for each node

view

Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)

main

Title of the plot

colorPalette

Color palette to use

symmetric

Plot colours symmetric around zero

Value

Nothing is returned. A plot is drawn in which each node is coloured depending on its value for the given variable

See Also

PlotMarker,PlotStars, PlotPies,PlotCenters, BuildMST

Examples

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

# Plot some random values
rand <- runif(flowSOM.res$map$nNodes)
PlotVariable(flowSOM.res,rand)