FlowSOM {FlowSOM} | R Documentation |
Method to run general FlowSOM workflow. Will scale the data and uses consensus meta-clustering by default.
FlowSOM( input, pattern = ".fcs", compensate = FALSE, spillover = NULL, transform = FALSE, toTransform = NULL, transformFunction = flowCore::logicleTransform(), scale = TRUE, scaled.center = TRUE, scaled.scale = TRUE, silent = TRUE, colsToUse, nClus = NULL, maxMeta, importance = NULL, seed = NULL, ... )
input |
a flowFrame, a flowSet or an array of paths to files or directories |
pattern |
if input is an array of file- or directorynames, select only files containing pattern |
compensate |
logical, does the data need to be compensated |
spillover |
spillover matrix to compensate with If NULL and compensate=TRUE, we will look for $SPILL description in fcs file. |
transform |
logical, does the data need to be transformed with a logicle transform |
toTransform |
column names or indices that need to be transformed.
If |
transformFunction |
Defaults to logicleTransform() |
scale |
logical, does the data needs to be rescaled |
scaled.center |
see |
scaled.scale |
see |
silent |
if |
colsToUse |
column names or indices to use for building the SOM |
nClus |
Exact number of clusters for meta-clustering.
If |
maxMeta |
Maximum number of clusters to try out for meta-clustering. Ignored if nClus is specified |
importance |
array with numeric values. Parameters will be scaled according to importance |
seed |
Set a seed for reproducible results |
... |
options to pass on to the SOM function (xdim, ydim, rlen, mst, alpha, radius, init, distf) |
A list
with two items: the first is the flowSOM object
containing all information (see the vignette for more detailed
information about this object), the second is the metaclustering of
the nodes of the grid. This is a wrapper function for
ReadInput
, BuildSOM
,
BuildMST
and MetaClustering
.
Executing them separately may provide more options.
scale
,ReadInput
,BuildSOM
,
BuildMST
,MetaClustering
# Read from file fileName <- system.file("extdata", "68983.fcs", package="FlowSOM") flowSOM.res <- FlowSOM(fileName, compensate=TRUE,transform=TRUE, scale=TRUE,colsToUse=c(9,12,14:18),nClus=10) # Or read from flowFrame object ff <- flowCore::read.FCS(fileName) ff <- flowCore::compensate(ff,ff@description$SPILL) ff <- flowCore::transform(ff, flowCore::transformList(colnames(ff@description$SPILL), flowCore::logicleTransform())) flowSOM.res <- FlowSOM(ff,scale=TRUE,colsToUse=c(9,12,14:18),nClus=10) # Plot results PlotStars(flowSOM.res$FlowSOM, backgroundValues = flowSOM.res$metaclustering) # Get metaclustering per cell flowSOM.clustering <- GetMetaclusters(flowSOM.res)