PlotClusters2D: PlotClusters2D

In saeyslab/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

PlotClusters2D

Description

Plot nodes on scatter plot

Usage

PlotClusters2D(
  fsom,
  marker1,
  marker2,
  nodes,
  col = "#FF0000",
  maxBgPoints = 10000,
  pchBackground = ".",
  pchCluster = ".",
  main = "",
  xlab = fsom$prettyColnames[marker1],
  ylab = fsom$prettyColnames[marker2],
  xlim = c(min(fsom$data[, marker1]), max(fsom$data[, marker1])),
  ylim = c(min(fsom$data[, marker2]), max(fsom$data[, marker2])),
  ...
)

Arguments

fsom	FlowSOM object, as generated by BuildMST
marker1	Marker to plot on the x-axis
marker2	Marker to plot on the y-axis
nodes	Nodes of which the cells should be plotted in red
col	Colors for all the cells in the selected nodes (ordered array)
maxBgPoints	Maximum number of background points to plot
pchBackground	Character to use for background cells
pchCluster	Character to use for cells in cluster
main	Title of the plot
xlab	Label for the x axis
ylab	Label for the y axis
xlim	Limits for the x axis
ylim	Limits for the y axis
...	Other parameters to pass on to plot

Details

Plot a 2D scatter plot. All cells of fsom$data are plotted in black, and those of the selected nodes are plotted in red. The nodes in the grid are indexed starting from the left bottom, first going right, then up. E.g. In a 10x10 grid, the node at top left will have index 91.

Value

Nothing is returned. A plot is drawn in which all cells are plotted in black and the cells of the selected nodes in red.

See Also

PlotNumbers, PlotCenters, BuildMST

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 <- ReadInput(fileName, compensate = TRUE, transform = TRUE,
                            scale = TRUE)
   flowSOM.res <- BuildSOM(flowSOM.res, colsToUse = c(9, 12, 14:18))
  flowSOM.res <- BuildMST(flowSOM.res)
   
   # Plot cells
   ## Not run: 
   Plot2DScatters(flowSOM.res, c(1, 2), clusters = 91)
   
## End(Not run)

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.