Package: cyanoFilter 1.13.0

Oluwafemi Olusoji

cyanoFilter: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.

Authors:Oluwafemi Olusoji [cre, aut], Aerts Marc [ctb], Delaender Frederik [ctb], Neyens Thomas [ctb], Spaak jurg [aut]

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cyanoFilter.pdf |cyanoFilter.html✨
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NEWS

# Install 'cyanoFilter' in R:
install.packages('cyanoFilter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fomotis/cyanofilter/issues

On BioConductor:cyanoFilter-1.13.0(bioc 3.20)cyanoFilter-1.12.0(bioc 3.19)

bioconductor-package

34 exports 0.71 score 128 dependencies 30 downloads

Last updated 2 months agofrom:ba8c0dbefc

Exports:accTestaccuracycellMarginclusterExtractclusterExtractpDebrisFilterdebrisNcfullFlowframegateFuncgetChannelggpairsDensggplotDensggplotDens2goodFcsis.DebrisFilteris.flowFrameis.flowSetis.MarginEventsis.PhytopFilterlnTransMarginEventsnewFlowframenoNAnoNegoneDgatepairsPlotphytoFilterPhytopFilterpigmentGateplotreducedFlowframeretainrowNumberssummaries

Dependencies:abindbackportsBHBiobaseBiocGenericsbitbit64bitopsbootbriobroombroom.helperscallrcarcarDatacaToolsclicliprcolorspacecowplotcpp11crayoncytolibcytometreedeldirdescdiffobjdigestdplyrevaluatefansifarverflowClustflowCoreflowDensityflowVizforcatsfsgenericsgeometryGGallyggplot2ggstatsglueGoFKernelgplotsgraphgtablegtoolshavenhexbinhmsIDPmiscigraphinterpisobandjpegjsonliteKernSmoothlabelinglabelledlatticelatticeExtralifecyclelinproglme4lpSolvemagicmagrittrMASSMatrixMatrixModelsmatrixStatsmclustmgcvminqamrfDepthmunsellnlmenloptrnnetnumDerivpatchworkpbkrtestpillarpkgbuildpkgconfigpkgloadplyrpngpolyclippraiseprettyunitsprocessxprogresspspurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenRcppProgressreadrrematch2reshape2Rhdf5librlangrprojrootRProtoBufLibS4VectorsscalesSparseMstringistringrsurvivaltestthattibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwaldowithr

cyanoFilter

Olusoji O. D., Spaak J., Neyens T.,De Laender F., Aerts M.

Rendered fromcyanoFilter.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2021-03-08
Started: 2020-09-30

Readme and manuals

Help Manual

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