FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data
Version 1.8.0

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

AuthorSofie Van Gassen, Britt Callebaut and Yvan Saeys
Bioconductor views CellBasedAssays CellBiology Clustering FlowCytometry Software Visualization
Date of publicationNone
MaintainerSofie Van Gassen <sofie.vangassen@ugent.be>
LicenseGPL (>= 2)
Version1.8.0
URL http://www.r-project.org http://dambi.ugent.be
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FlowSOM")

Popular man pages

computeBackgroundColor: Internal function for computing background nodes
FlowSOM: Run the FlowSOM algorithm
FlowSOMSubset: FlowSOM subset
FMeasure: F measure
MetaClustering: MetaClustering
PlotMarker: Plot marker values
PlotNode: Plot star chart
See all...

All man pages Function index File listing

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
computeBackgroundColor: Internal function for computing background nodes
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
PlotCenters: Plot cluster centers on a 2D plot
PlotClusters2D: Plot nodes on scatter plot
PlotGroups: Plot differences between groups
PlotMarker: Plot marker values
PlotNode: Plot star chart
PlotNumbers: Plot the index of each node
PlotPies: Plot comparison with other clustering
plotStarLegend: Plot legend for star plot
PlotStars: Plot 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

Functions

Files

DESCRIPTION
NAMESPACE
R
R/0_FlowSOM.R
R/1_readInput.R
R/2_buildSOM.R
R/3_buildMST.R
R/4_metaClustering.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/FlowSOM.R
inst/doc/FlowSOM.Rnw
inst/doc/FlowSOM.pdf
inst/extdata
inst/extdata/lymphocytes.fcs
inst/extdata/manualGating.xml
man
man/AddFlowFrame.Rd
man/AggregateFlowFrames.Rd
man/BuildMST.Rd
man/BuildSOM.Rd
man/CountGroups.Rd
man/Dist.MST.Rd
man/FMeasure.Rd
man/FlowSOM.Rd
man/FlowSOMSubset.Rd
man/Initialize.Rd
man/MapDataToCodes.Rd
man/MetaClustering.Rd
man/NewData.Rd
man/PlotCenters.Rd
man/PlotClusters2D.Rd
man/PlotGroups.Rd
man/PlotMarker.Rd
man/PlotNode.Rd
man/PlotNumbers.Rd
man/PlotPies.Rd
man/PlotStars.Rd
man/PlotVariable.Rd
man/ProcessGatingML.Rd
man/Purity.Rd
man/QueryStarPlot.Rd
man/ReadInput.Rd
man/SOM.Rd
man/SaveClustersToFCS.Rd
man/UpdateNodeSize.Rd
man/computeBackgroundColor.Rd
man/metaClustering_consensus.Rd
man/plotStarLegend.Rd
src
src/som.c
vignettes
vignettes/FlowSOM.Rnw
FlowSOM documentation built on May 20, 2017, 9:36 p.m.

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