The exported FCS files then often end up with some markers being transformed (sometimes this affects the most recently opened marker alone, sometimes this affects nearly all of the markers). The biexponential transformation is applied to some of the data when our wet-lab folks open and start gating the data. I'm a relative novice when it comes to flow data, and I have a couple of general questions about shifting the data from FlowJo to R and performing the pre-processing steps. This data is then delivered to our computational group for additional analysis. Of $SPILL description in fcs file will be used.Scientists that perform the benchwork and acquisition of flow cytometry data at my institute export FCS files from FlowJo after both compensating the data and removing dead cells/populations that are not of interest. If NULL and transform= TRUE, column names Logical, does the data need to be transformedĬolumn names or indices that need to be transformed. Logical, does the data need to be compensated If input is an array of file- or directorynames, ReadInput ( input, pattern = ".fcs", compensate = FALSE, spillover = NULL, transform = FALSE, toTransform = NULL, transformFunction = flowCore :: logicleTransform (), scale = FALSE, scaled.center = TRUE, scaled.scale = TRUE, silent = FALSE )Ī flowFrame, a flowSet or an array of paths to files UpdateNodeSize: Update nodesize of FlowSOM object.TestOutliers: Test if any cells are too far from their cluster centers.SaveClustersToFCS: Write FlowSOM clustering results to the original FCS files.ReadInput: Read fcs-files or flowframes.
QueryStarPlot: Query a certain cell type.Purity: Calculate mean weighted cluster purity.PlotVariable: Plot a variable for all nodes.plotStarLegend: Plot legend for star plot.PlotPies: Plot comparison with other clustering.PlotOverview2D: Plot metaclusters on scatter plots.PlotNumbers: Plot the index of each node.PlotGroups: Plot differences between groups.PlotClusters2D: Plot nodes on scatter plot.PlotCenters: Plot cluster centers on a 2D plot.NewData: Map new data to a FlowSOM grid.metaClustering_consensus: MetaClustering.MapDataToCodes: Assign nearest node to each datapoint.Initialize_PCA: Create a grid from first 2 PCA components.Initialize_KWSP: Select k well spread points from X.GetMFIs: Get MFI values for all clusters.GetMetaclusters: Get metacluster label for all individual cells.GetFlowJoLabels: Process a flowjo workspace file.GetClusters: Get cluster label for all individual cells.Dist.MST: Calculate distance matrix using a minimal spanning tree.CountGroups: Calculate differences in cell counts between groups.computeBackgroundColor: Internal function for computing background nodes.AggregateFlowFrames: Aggregate multiple fcs files together.AddFlowFrame: Add a flowFrame to the data variable of the FlowSOM object.
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