FlowSOM (version 1.4.0)

PlotStarsSD: Plot standard deviation star charts

Description

Plot FlowSOM grid or tree, where each node is represented by a star chart indicating standard deviation of the marker values

Usage

PlotStarsSD(fsom, markers = fsom$map$colsUsed, view = "MST", colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")), backgroundValues = NULL, backgroundColor = function(n) {     grDevices::rainbow(n, alpha = 0.3) }, backgroundLim = NULL, legend = TRUE, query = NULL, main = "")

Arguments

fsom

FlowSOM object, as generated by BuildMST

markers

Array of markers to use. Default: the markers used to build the tree

view

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

colorPalette

Colorpalette to be used for the markers

backgroundValues

Values to be used for background coloring, either numerical values or something that can be made into a factor (e.g. a clustering)

backgroundColor

Colorpalette to be used for the background coloring . Can be either a function or an array specifying colors

backgroundLim

Only used when backgroundValues are numerical. Defaults to min and max of the backgroundValues.

legend

Logical, if TRUE add a legend

query

Show a low/high profile for certain markers in the legend. See also QueryStarPlot

main

Title of the plot

Value

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

See Also

PlotStars

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