Add support for flowSets in CytoNorm

[DillonHammill]

Hi @SofieVG,

I have made some changes to the CytoNorm code base to add support for it within CytoExploreR.

Here is a summary of the changes:

• add support for flowSets as inputs for CytoNorm.train() and CytoNorm.normalize(). This required adding similar support for FlowSOM::AggregateFlowFrames(), I have submitted a separate PR for those changes.
• CytoNorm.normalize() now returns the normalized flowSet.
• CytoNorm.normalize() gains a new write argument to optionally write the normalized data to new FCS files, this is set to TRUE by default for consistency with old behaviour.
• I came across an error when running the evaluation examples, I have fixed that as well.

I have run all examples and tested the code on flowSets and everything behaves as it should.

Please let me know if there are any additional modifications you would like me to make.

Cheers, Dillon

[SofieVG]

Hi Dillon,

I made a small adaptation to only return a flowSet from Cytonorm.normalize when a flowSet was given as input. When normalizing a set of files from directory, they are not always guaranteed to have the same columns (some might have additional columns not used for the normalization), which gives an error when converting to a flowSet at the end. Can you check whether it still works as expected for you with this change?