Breaking Changes - ggplot2 and ggcyto updates

[DavidRach]

Hello All,

With ggplot2 switching to S7 internals, ggcyto broke last fall. For context, see here for initial issue, here for intermediate and here for main resolution.

With ggcyto now apparently stable, checked to see whether BiocManager installed flowGate works with both current ggplot2 version and ggcyto dev versions, but encountered errors upon the Shiny launch.

I documented the process of identifying and resolving the issues in my forked branch here. The two main issues appear to be a residual ggcyto_GatingSet class that is causing as.ggplot() to error out

And also an internal change in ggplot2 that places data in a different access location, causing the retrieval of the axis names for adding the gate back to the GatingSet to error out.

Not sure if this repository is monitored (showing flowGate as developmental vs Bioconductors 1.10.0), so will also email you to make sure someone sees it.

Thanks once again for all your efforts on flowGate, I really appreciate the effort that went into it (including the biexponential transform translation layer!)

Best Wishes-
David