UpdateNodeSize: Update nodesize of FlowSOM object

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

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", "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)

# 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)

FlowSOM documentation built on Nov. 8, 2020, 6:40 p.m.