PlotOverview2D {FlowSOM} | R Documentation

## PlotOverview2D

### Description

Plot metaclusters on scatter plots

### 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

### Details

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.

### 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

       ## Deprecated - use Plot2DScatters instead ##

       # 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

       ## Not run:
         png("Markeroverview.png",
             width = 500 * length(markers_of_interest),
             height = 500 * length(metaclusters_of_interest))
         Plot2DScatters(flowSOM.res,
                        channelpairs = markers_of_interest,
                        metaclusters = metaclusters_of_interest)
         dev.off()

    ## End(Not run)

[Package FlowSOM version 2.2.0 Index]