PlotStars: Plot star charts

Description Usage Arguments Value See Also Examples

View source: R/3_buildMST.R

Description

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

Usage

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PlotStars(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,
  backgroundBreaks = NULL, thresholds = 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.

backgroundBreaks

Breaks to pass on to cut, to split numerical background values. If NULL, the length of backgroundColor will be used (default 100).

thresholds

Optional. Array containing a number for each of the markers to be used as the split between high/low. If provided, the percentage of positive cells is indicated instead of the MFI

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 median fluorescence intensities. Resets the layout back to 1 plot at the end.

See Also

PlotPies,PlotMarker, PlotCenters, BuildMST

Examples

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   # 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)


FlowSOM documentation built on May 20, 2017, 9:36 p.m.
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