PlotOverview2D {FlowSOM} | R Documentation |
Write multiple 2D scatter plots to a png file. All cells of fsom$data are plotted in black, and those of the selected metaclusters are plotted in color.
PlotOverview2D(fsom, markerlist, metaclusters, colors = NULL, ff, ...)
fsom |
FlowSOM object, as generated by |
markerlist |
List in which each element is a pair of marker names |
metaclusters |
Metaclusters of interest |
colors |
Named vector with color value for each metacluster. If NULL (default) colorbrewer "paired" is interpolated |
ff |
flowFrame to use as reference for the marker names |
... |
Other parameters to pass on to PlotClusters2D |
Nothing is returned, but a plot is drawn for every markerpair and every metacluster. The individual cells are colored, and the center of each FlowSOM cluster is indicated with a blue cross.
# Read from file, build self-organizing map and minimal spanning tree fileName <- system.file("extdata", "68983.fcs", package="FlowSOM") flowSOM.res <- FlowSOM(fileName, compensate=TRUE, transform=TRUE, scale=TRUE, colsToUse=c(9,12,14:18), nClus = 10, seed = 1) # Plot cells markers_of_interest = list(c("FSC-A", "SSC-A"), c("CD3", "CD19"), c("TCRb", "TCRyd"), c("CD4", "CD8")) metaclusters_of_interest = 1:10 # Recommended to write to png png("Markeroverview.png", width = 500 * length(markers_of_interest), height = 500 * length(metaclusters_of_interest)) PlotOverview2D(flowSOM.res, markerlist = markers_of_interest, metaclusters = metaclusters_of_interest, pchCluster = 19, ff = flowCore::read.FCS(fileName)) dev.off()