PlotMarker {FlowSOM} | R Documentation |
Plot comparison with other clustering
PlotMarker( fsom, marker, refMarkers = fsom$map$colsUsed, title = GetMarkers(fsom, marker), colorPalette = FlowSOM_colors, lim = NULL, ... )
fsom |
FlowSOM object |
marker |
A vector of markers/channels to plot. |
refMarkers |
Is used to determine relative scale of the marker that will be plotted. Default are all markers used in the clustering. |
title |
A vector with custom titles for the plot. Default is the marker name. |
colorPalette |
Colorpalette to use. Can be a function or a vector. |
lim |
Limits for the scale |
... |
Additional arguments to pass to |
Plot FlowSOM grid or tree, coloured by node values for a specific marker
A ggplot figure is returned in which every cluster is colored according to the MFI value for the specified marker
# Build FlowSOM model fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM") flowSOM.res <- FlowSOM(fileName, compensate = TRUE, transform = TRUE, scale = FALSE, colsToUse = c(9, 12, 14:18), nClus = 10, seed = 1) # Plot one marker PlotMarker(flowSOM.res, "CD19") PlotMarker(flowSOM.res, "CD19", colorPalette = c("grey", "red")) # Plot all markers PlotMarker(flowSOM.res, c(9, 12, 14:18)) # Use specific limits if the ones from the columns used for clustering # are not relevant for your marker of choice PlotMarker(flowSOM.res, "FSC-A", lim = c(55000, 130000)) # Example with additional FlowSOM plotting options PlotMarker(flowSOM.res, "CD19", view = "grid", equalNodeSize = TRUE, backgroundValues = 1:100 == 27, backgroundColors = c("white", "red"))