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

In nolanlab/spade: SPADE -- An analysis and visualization tool for Flow Cytometry

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

Author(s)

Michael Linderman

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"))

nolanlab/spade documentation built on May 23, 2019, 9:32 p.m.