SPADE.addDensityToFCS: Annotate FCS file with local density of each observation
In olimora/mySPADE: SPADE -- An analysis and visualization tool for Flow Cytometry

Description Usage Arguments Value Author(s) Examples

Compute the local density of observation and incorporate the result as a new parameter to the FCS file. The local density is modeled as an integer count of the number of other observations within a specified distance of the observation.

1	SPADE.addDensityToFCS(infilename, outfilename, cols = NULL, arcsinh_cofactor=NULL, transforms=flowCore::arcsinhTransform(a=0, b=0.2), kernel_mult = 5, apprx_mult = 1.5, med_samples = 2000, comp=TRUE)

`infilename`	Name of the input FCS file
`outfilename`	Name of the output FCS file
`cols`	Usually a vector of strings specifying the columns to be used in the density calculation, e.g., c("(Cd110)D","(Cs111)D"). Strings will be matched against the parameter names extracted from the FCS file. The default=NULL will use all parameters.
`arcsinh_cofactor`	DEPRECATED. Cofactor used in arcsinh transform `asinh(data/arcsinh_cofactor)` of data.
`transforms`	Transform object to apply to data. A single transform object will be applied to all channels. To apply different transforms to specific channels use a named vector of transform objects (where names are parameter names).
`kernel_mult`	Multiplier of the minimum median distance within which other observations are counted towards the density
`apprx_mult`	Multiplier of the minimum median distance within which observations are approximated to have the same density
`med_samples`	Number of observations used to estimate the minimum median distance
`comp`	Apply compensation matrix if present in SPILL or SPILLOVER keywords

The name of the written file is returned

Michael Linderman

	# Not run
	## Load two-parameters sample data included in package
	#data_file_path = paste(installed.packages()["spade","LibPath"],"spade","extdata","SimulatedRawData.fcs",sep=.Platform$file.sep)
	#
	#output_dir <- tempdir()
	#
	## Compute and annotate FCS file with density
	#density_file_path <- paste(output_dir,.Platform$file.sep,basename(data_file_path),".density.fcs",sep="")
	#SPADE.addDensityToFCS(data_file_path, density_file_path, cols=c("marker1","marker2"))