PlotStars {FlowSOM} | R Documentation |
Plot FlowSOM grid or tree, where each node is represented by a star chart indicating median marker values
PlotStars( fsom, markers = fsom$map$colsUsed, view = "MST", colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")), starBg = "white", backgroundValues = NULL, backgroundColor = function(n) { grDevices::rainbow(n, alpha = 0.3) }, backgroundLim = NULL, backgroundBreaks = NULL, backgroundSize = NULL, thresholds = NULL, legend = TRUE, query = NULL, range = "all", main = "" )
fsom |
FlowSOM object, as generated by |
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 |
starBg |
Background color inside the star circle. Default is "white". Can also be put to "transparent" (as was the case for older versions). |
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 |
backgroundSize |
Size of the background circles. Default 15. |
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 |
range |
If "all" (default), range is computed on all markers passed, if "one", range is computed on every marker separately. The height of the pie pieces will be computed relative to this range. |
main |
Title of the plot |
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.
PlotPies
,PlotMarker
,
PlotCenters
, BuildMST
# Read from file, build self-organizing map and minimal spanning tree fileName <- system.file("extdata", "68983.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)