censusFile: Create a consensus from several classification vector files...

In armbrustlab/flowPhyto: Methods for Continuous Flow Cytometry

Description

Create a consensus from several classification vectors, cross tabulate the population composition and save an image of the cytograms

Usage

censusFile(opp.path, map.margin=2, output.path=getCruisePath(opp.path), 
		def.path=paste(getCruisePath(opp.path),'pop.def.tab',sep=''), transform=TRUE)

Arguments

opp.path	Path to OPP event file.
map.margin	Margin in latitude/longitude around the map plots.
output.path	Path to the directory where you wish to output data.
def.path	Path to the file that defines how to gate & cluster the events into populations.
transform	To save the cytograms as log-transformed data

Value

a one dimentional consensus vector file (one column) and a one dimentional cross tabulation file (one row) both writen to disk

Examples

example.cruise.name <- 'seaflow_cruise'
temp.dir <- '.'

seaflow.path <- system.file("extdata", example.cruise.name, package="flowPhyto")
file.copy(from=seaflow.path, to=temp.dir, recursive=TRUE)

#opp.in.path <- system.file("extdata","seaflow_cruise","2011_001", "1.evt.opp", 
#					package="flowPhyto")

opp.out.path <- paste(temp.dir,'/',example.cruise.name,'/2011_001/1.evt.opp',sep='')
censusFile(opp.path=opp.out.path, map.margin=.5)
unlink(example.cruise.name, recursive=TRUE)

armbrustlab/flowPhyto documentation built on May 10, 2019, 1:40 p.m.