UpdateNodeSize {FlowSOM} | R Documentation

## Update nodesize of FlowSOM object

### Description

Add size property to the graph based on cellcount for each node

### Usage

    UpdateNodeSize(fsom, count = NULL, reset = FALSE, transform = sqrt,
      maxNodeSize = 15, shift = 0, scale = NULL)

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`count` | Absolute cell count of the sample
`reset` | Logical. If `TRUE`, all nodes get the same size
`transform` | Transformation function. Use e.g. square root to let counts correspond with area of node instead of radius
`maxNodeSize` | Maximum node size after rescaling. Default: 15
`shift` | Shift of the counts, defaults to 0
`scale` | Scaling of the counts, defaults to the maximum of the value minus the shift. With shift and scale set as default, the largest node will be maxNodesize and an empty node will have size 0

### Value

Updated FlowSOM object

### See Also

`BuildMST`

### Examples

    # Read from file, build self-organizing map and minimal spanning tree
    fileName <- system.file("extdata","lymphocytes.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)

    # Give all nodes same size
    flowSOM.res <- UpdateNodeSize(flowSOM.res,reset=TRUE)
    PlotStars(flowSOM.res)

    # Node sizes relative to amount of cells assigned to the node
    flowSOM.res <- UpdateNodeSize(flowSOM.res)
    PlotStars(flowSOM.res)

    # Smaller node sizes
    flowSOM.res <- UpdateNodeSize(flowSOM.res, maxNodeSize = 5)
    PlotStars(flowSOM.res)

[Package FlowSOM version 1.12.0 Index]