Description Usage Arguments Value Examples
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.
1 | 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)
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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 |
1) A vector file composed of one single column indicating population assignment of each particle. 2) Cytograms showing the phytoplankton populations
1 2 3 4 5 6 | 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
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