clusterPop: Rea-time clustering of phytoplankton populations from the...

Description Usage Arguments Value Examples

Description

The package analyzes a continuous series of OPP files collected by SeaFlow. The package performs classification of plankton populations based on k-means clustering algorithm and customizable parameters used to define the pre-gating regions.

Usage

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clusterPop(opp.filelist, save.path = getCruisePath(opp.filelist), pop.def.path, test=F, lim.largeP = NULL, tol=0.1, h0=0.5, h=1.0, min.opp = 800, min.beads = 200, min.synecho=200,  lim.beads = 0, lim.synecho =0, lim.debris=c(10000,4000), save.plot=F)

Arguments

opp.filelist

list of OPP files

save.path

Path to the directory where you wish to output data. Cruise folder by default

pop.def.tab

Path to the file that defines how to gate & cluster the populations defined in pop.baseline.

test

Cluster the first OPP file of the list to set up the parameters.

lim.largeP

Minimal size for large particles with low red fluorescence

tol

Peaks merging tolerance level makes the density function of all modes similar to each other. See flowPeaks package for details. Default is 0.2

h0

Scaling factor of the common variance matrix makes the density function smoother. See flowPeaks package for details. Default is 0.5

h

Scaling factor of the individual variance matrix makes neighboring peaks merging easier. See flowPeaks package for details. Default is 1.0

min.opp

Minimum number of cells for clustering. Default is 800

min.beads

Minimum number of beads for reference. Default is 150

min.synecho

Minimum number of Synechococcus for reference, if beads number not sufficient. Default is 200

diff.lim.beads

correction for size reference from beads. Default is 0

lim.synecho

correction for size reference from Synechococcus. Default is 0

lim.noise

Chl_small median and fsc_small width minima of Small phytoplankton. If below, population converted to 'noise'. Default is c(10000,4000)

save.plot

whether saving the cytograms showing the output of the classification. Default is FALSE

Value

1) A vector file composed of one single column indicating population assignment of each particle. 2) Cytograms showing the phytoplankton populations

Examples

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example.cruise.name <- 'seaflow_cruise'
seaflow.path <- system.file("extdata", example.cruise.name, package="flowPhyto")
pop.path <- system.file("extdata", example.cruise.name, 'pop.def.tab',package="flowPhyto")
save.path <- '.'

# TO BE DONE

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