PlotOverview2D {FlowSOM} | R Documentation

## Plot metaclusters on scatter plots

### Description

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.

### Usage

    PlotOverview2D(fsom, markerlist, metaclusters, colors = NULL, ff, ...)

### Arguments

`fsom` | FlowSOM object, as generated by `FlowSOM`. If using a FlowSOM object as generated by `BuildMST`, it needs to be wrapped in a list, list(FlowSOM = fsom, metaclustering = metaclustering).
`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

### Value

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.

### See Also

`PlotClusters2D`

### Examples

       # 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()

[Package FlowSOM version 1.18.0 Index]