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SofieVG / FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data
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GetFlowJoLabels #63

Open Aminach1 opened 7 months ago

Aminach1 commented 7 months ago

Hello,

Thank you for the great package!

I wanted to extract the manual labels with the function "GetFlowJoLabels" so that I can establish a comparison between manual and automated. Unfortunately, I got the error message: Error in manualMatrix[, cellType] : subscript out of bounds

gatingResult <- GetFlowJoLabels(fcs.dir, wspFile, cellTypes = cellTypes, getData = TRUE, sample_names_from="sampleNode")

Do you have any ideas how I could solve this? Thank you!

gmillerscripps commented 6 months ago

Hi @Aminach1 are you confident that all of your cellTypes are present in the flowJo workspace?

You could start with: 

gatingResult <- GetFlowJoLabels(fcs.dir, wspFile,
cellTypes = NULL,
getData = TRUE, sample_names_from="sampleNode")

and then look at: print(levels(gatingResult[["manual"]])) to determine if your cellTypes are present.

Hope this helps. If this works, I am curious to know if the results match the gated numbers that you see in your flowJo workspace.