FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

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FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.

Author
Sofie Van Gassen, Britt Callebaut and Yvan Saeys
Date of publication
None
Maintainer
Sofie Van Gassen <sofie.vangassen@ugent.be>
License
GPL (>= 2)
Version
1.6.0
URLs

View on Bioconductor

Man pages

AddFlowFrame
Add a flowFrame to the data variable of the FlowSOM object
AggregateFlowFrames
Aggregate multiple fcs files together
BuildMST
Build Minimal Spanning Tree
BuildSOM
Build a self-organizing map
CountGroups
Calculate differences in cell counts between groups
Dist.MST
Calculate distance matrix using a minimal spanning tree...
FlowSOM
Run the FlowSOM algorithm
FlowSOMSubset
FlowSOM subset
FMeasure
F measure
Initialize
Select k well spread points from X
MapDataToCodes
Assign nearest node to each datapoint
MetaClustering
MetaClustering
metaClustering_consensus
MetaClustering
NewData
Map new data to a FlowSOM grid
PeaksAndValleys
Find peaks and valleys in one-dimensional data
PlotCenters
Plot cluster centers on a 2D plot
PlotClusters2D
Plot nodes on scatter plot
PlotGroups
Plot differences between groups
PlotMarker
Plot marker values
PlotNumbers
Plot the index of each node
PlotPies
Plot comparison with other clustering
plotStarLegend
Plot legend for star plot
PlotStars
Plot star charts
PlotStarsSD
Plot standard deviation star charts
PlotVariable
Plot a variable for all nodes
ProcessGatingML
Process a gatingML file
Purity
Calculate mean weighted cluster purity
QueryStarPlot
Query a certain cell type
ReadInput
Read fcs-files or flowframes
SaveClustersToFCS
Write FlowSOM clustering results to the original FCS files
SOM
Build a self-organizing map
UpdateNodeSize
Update nodesize of FlowSOM object

Files in this package

FlowSOM/DESCRIPTION
FlowSOM/NAMESPACE
FlowSOM/R
FlowSOM/R/0_FlowSOM.R
FlowSOM/R/1_readInput.R
FlowSOM/R/2_buildSOM.R
FlowSOM/R/3_buildMST.R
FlowSOM/R/4_metaClustering.R
FlowSOM/build
FlowSOM/build/vignette.rds
FlowSOM/inst
FlowSOM/inst/NEWS
FlowSOM/inst/doc
FlowSOM/inst/doc/FlowSOM.R
FlowSOM/inst/doc/FlowSOM.Rnw
FlowSOM/inst/doc/FlowSOM.pdf
FlowSOM/inst/extdata
FlowSOM/inst/extdata/lymphocytes.fcs
FlowSOM/inst/extdata/manualGating.xml
FlowSOM/man
FlowSOM/man/AddFlowFrame.Rd
FlowSOM/man/AggregateFlowFrames.Rd
FlowSOM/man/BuildMST.Rd
FlowSOM/man/BuildSOM.Rd
FlowSOM/man/CountGroups.Rd
FlowSOM/man/Dist.MST.Rd
FlowSOM/man/FMeasure.Rd
FlowSOM/man/FlowSOM.Rd
FlowSOM/man/FlowSOMSubset.Rd
FlowSOM/man/Initialize.Rd
FlowSOM/man/MapDataToCodes.Rd
FlowSOM/man/MetaClustering.Rd
FlowSOM/man/NewData.Rd
FlowSOM/man/PeaksAndValleys.Rd
FlowSOM/man/PlotCenters.Rd
FlowSOM/man/PlotClusters2D.Rd
FlowSOM/man/PlotGroups.Rd
FlowSOM/man/PlotMarker.Rd
FlowSOM/man/PlotNumbers.Rd
FlowSOM/man/PlotPies.Rd
FlowSOM/man/PlotStars.Rd
FlowSOM/man/PlotStarsSD.Rd
FlowSOM/man/PlotVariable.Rd
FlowSOM/man/ProcessGatingML.Rd
FlowSOM/man/Purity.Rd
FlowSOM/man/QueryStarPlot.Rd
FlowSOM/man/ReadInput.Rd
FlowSOM/man/SOM.Rd
FlowSOM/man/SaveClustersToFCS.Rd
FlowSOM/man/UpdateNodeSize.Rd
FlowSOM/man/metaClustering_consensus.Rd
FlowSOM/man/plotStarLegend.Rd
FlowSOM/src
FlowSOM/src/som.c
FlowSOM/vignettes
FlowSOM/vignettes/FlowSOM.Rnw