Man pages for armbrustlab/flowPhyto
Methods for Continuous Flow Cytometry
| census | Cross tabulate a consensus vector |
| censusFile | Create a consensus from several classification vector files... |
| 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... |
| 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... |
| createResamplingScheme | Generate the Population Resampling scheme. |
| EVT.HEADERS | Seaflow File Headers |
| filter | Filter Optimally Positioned Particles from an EVT dataframe |
| filterFile | Filter an EVT file and output an Optimally Positioned... |
| getCruiseFiles | Get all of the files from a cruise. |
| getCruisePath | Get the Cruise Directory. |
| getFileNumber | Get the (original) integer file number of any seaflow... |
| joinSDS | join this dataframe to the corresponding SDS log file entry. |
| OPPtoFCSconversion | Convert OPP files into FCS 3.0. |
| 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... |
| validatePopDef | Validate a Population Definition Dataframe. |
| writeSeaflow | Write A SeaFlow File |
