classify: Cluster the different Phytoplankton Populations

In armbrustlab/flowPhyto: Methods for Continuous Flow Cytometry

Description

Classify the different cell populations from an OPP or FCS dataframe according to a pre-defined parameters of population definition

Because the characteristics of each phytoplankton populations varied according to environmental conditions and instrument settings, a customizable table of pre-defined parameters (pop.def) is used to help in gating the different phytoplankton populations. The rows of the pop.def table represent the names of the different populations. The columns of the pop.def table represent the parameters used for gating and clustering the different populations. The function uses these pre-defined parameters and inputs a single OPP or FCS file to cluster cell populations using flowMeans package

Usage

classify(x, pop.def=POP.DEF, varnames = CHANNEL.CLMNS.SM, numc=0, noise=0,  auto.correction=FALSE, plot.cluster=FALSE, plot.assignment=FALSE, try.context='local',...)

Arguments

x	an OPP or FCS dataframe.
pop.def	pop.def table that defines how to gate & cluster the events into populations.
varnames	A character vector specifying the variables (columns) to be included in clustering when choosing flowMeans.
numc	Number of clusters when choosing flowMeans. If set to 0 (default) the value matches the number of populations defined in pop.def table . If set to NA, the optimal number of clusters will be estimated automatically.
noise	Set up the noise threshold for phytoplankton cells. Only cells with chlorophyll value higher than the noise will be clustered
auto.correction	Correct for potential mislabeling of phytoplankton populations defined in pop.def.tab
plot.cluster	Plot the output of clustering when choosing flowMeans
plot.assignment	Plot the output of Matching cluster number with cell population defined in pop.def.tab when choosing flowMeans
try.context	Default value set up to 'local'
...	additional arguments to be passed to the plot function

Value

an OPP or FCS dataframe like the input x but with an additional column 'pop' indicating population assignment

Examples

## reading a standard SeaFlow file
opp.path <- system.file("extdata","seaflow_cruise","2011_001", "1.evt.opp", 
				package="flowPhyto")
pop.def.path <- system.file("extdata","seaflow_cruise","pop.def.tab", 
				package="flowPhyto")

opp <- readSeaflow(opp.path)
def <- readPopDef(pop.def.path)
pop <- classify(x=opp, pop.def= def)

table(pop$pop)

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