PlotSD {FlowSOM} | R Documentation |
— Function in development, use with caution — Plot FlowSOM grid or tree, coloured by standard deviaton
PlotSD( fsom, marker = NULL, view = "MST", main = NULL, colorPalette = grDevices::colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000")), symmetric = FALSE, lim = NULL, backgroundValues = NULL, backgroundColor = function(n) { grDevices::rainbow(n, alpha = 0.3) }, backgroundLim = NULL, backgroundBreaks = NULL )
fsom |
FlowSOM object, as generated by |
marker |
If a marker is given, the sd for this marker is shown. Otherwise, the maximum ratio is used. |
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 |
lim |
Variable limits |
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 |
From suggestion in email: I am currently considering a way to summarize for each node all the SD as one value. After computing the SD matrix (nrow = # nodes, ncol = # markers), I compute the median value per column, then divide the SD matrix by it, and finally take the maximum ratio of each line (aka node). Doing so I got a unique dispersion score per node.
Nothing is returned. A plot is drawn in which each node is coloured depending on its standard deviation
PlotMarker
,PlotStars
,
PlotPies
,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) PlotSD(flowSOM.res)