spade (version 1.20.0)

SPADE.addDensityToFCS: Annotate FCS file with local density of each observation

Description

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.

Usage

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)

Arguments

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

Value

The name of the written file is returned

Examples

	# 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"))