Methods for Continuous Flow Cytometry


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Documentation for package ‘flowPhyto’ version 1.8.0

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census Cross tabulate a consensus vector
censusFile Create a consensus from several classification vector files and cross tabulate the population composition
CHANNEL.CLMNS Seaflow detector column names
CHANNEL.CLMNS.SM Seaflow detector column names
classify Cluster the different Phytoplankton Populations
classifyFile Cluster the different Phytoplankton Populations
cleanupLogs Remove R Batch Output Files.
clearOutputs Clear the output files from particular flowPhyto pipeline steps.
combineCensusFiles Combine the Census Files.
combineSdsFiles Combine the SDS files.
consensus create a consensus vector from several classification vectors
consensusFile Create a consensus from several classification vector files and cross tabulate the population composition
createResamplingScheme Generate the Population Resampling scheme.
EVT.HEADER Seaflow File Headers
filter Filter Optimally Positioned Particles from an EVT dataframe
filterFile Filter an EVT file and output an Optimally Positioned Particles (OPP) file
getCruiseFiles Get all of the files from a cruise.
getCruisePath Get the Cruise Directory.
getFileNumber Get the (original) integer file number of any seaflow repository file.
joinSDS join this dataframe to the corresponding SDS log file entry.
pipeline Run the SeaFlow Pipeline
plotCruiseStats Plot a seaflow cruise statistics
plotCytogram Plot a Phytoplankton Cytogram
plotLatLongMap plot file location on a map
plotStatMap plot the stat.tab file on a map
POP.DEF population definition table
readConsensusFile Read a Consensus File.
readPopDef Read the Population Definition File.
readSeaflow Read a SeaFlow File
REPO.PATH Seaflow Data directory
summarize Summarize phytoplankon event & log parameters
summarizeFile Compute aggregate statistics on a collection of opp or fcs files.
validatePopDef Validate a Population Definition Dataframe.
writeSeaflow Write A SeaFlow File