# Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

## Documentation for package ‘cyanoFilter’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

accTest | tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.
accuracy | samples two rows in a matrix and check if the samples are similar or different based on their cluster labels
cellMargin | Removes or assign indicators to margin events.
clusterExtract | extract clusters based on supplied cluster indicator
clusterExtractp | takes a flowframe, name of cluster column and extracts part of flowframe that makes up proportion.
cyanoFilter | cyanoFilter: A package to identify and cluster phytoplankton cells contained in flow cytometry data.
DebrisFilter | the Debris class
debrisNc | gates out or assign indicators to debris particle based on their chlorophyll expression.
fullFlowframe | generic function for extracting the full flowframe
fullFlowframe-method | accesor method for reduced flowframe (DebrisFilter class)
fullFlowframe-method | accesor method for the fullflowframe (MarginEvent class)
fullFlowframe-method | accesor method for full flowframe(PhytoFilter class)
gateFunc | tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.
getChannel | returns the channel with more than one peak present. It returns NA if there is only one peak present.
ggpairsDens | produces a scatter plot of the expression matrix of the flowframe. If a cluster variable is given, it assigns different colors to the clusters.
ggplotDens | plots two channels of a flowframe.
ggplotDens2 | plots two channels of a flowframe with different colors for clusters identified.
goodFcs | indicates if measurement from a flowfile is good or bad.
is.DebrisFilter | function to check if object is of class cyanoFilter(DebrisFilter)
is.flowFrame | function to check if object is a flowFrame
is.flowSet | function to check if object is a flowSet
is.MarginEvents | function to check if object is of class cyanoFilter(MarginEvents)
is.PhytopFilter | function to check if object is of class cyanoFilter(PhytoFilter)
lnTrans | log transforms the expression matrix of a flowframe
MarginEvents | the marginEvent class
newFlowframe | takes a flowframe, a group indicator and formulates another flowframe with group indicator as part of the expression matrix of the new flowframe.
noNA | Removes NA values from the expression matrix of a flow cytometer file.
noNeg | Removes negative values from the expression matrix
oneDgate | returns the labels stating the cluster of each row in a flowfile.
pairsPlot | produces a scatter plot of the expression matrix of a flowframe. Note that, it takes some time to display the plot.
phytoFilter | gates out and assign indicators to phytoplankton cells based on the expression of measured cell complexity channels.
PhytopFilter | the phytofilter class
pigmentGate | gates out or assign indicators to phytoplankton cells based on the expression of the measured pigments.
plot-method | plot method for DebrisFilter objects
plot-method | plot method for MarginEvents objects
plot-method | plot method for PhytoFilter objects
reducedFlowframe | generic function for extracting the full flowframe
reducedFlowframe-method | accesor method for reduced flowframe (DebrisFilter class)
reducedFlowframe-method | accesor method for reduced flowframe (MarginEvent class)
reducedFlowframe-method | accesor method for reduced flowframe(PhytoFilter class)
retain | Decides if a file should be retiained or removed based on its status.
rowNumbers | returns the position of the cells below, above or between estimated gates
summaries | takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster
summaries-method | takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster
summaries-method | takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster
summaries-method | takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster