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RGLab / openCyto

A package that provides data analysis pipeline for flow cytometry.
GNU Affero General Public License v3.0
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simplify 'pop' column in csv template #156

Closed mikejiang closed 6 years ago

mikejiang commented 6 years ago

Maybe it is time for us to consider restricting pop as a simple and generic quadrant-pattern-only string (e.g. ++, +), @gfinak ? I know it will have some backward compatibility issue with the legacy template, but just felt it has been the known culprit in the past. We had enough questions and problems caused by it. (e.g. https://github.com/RGLab/openCyto/issues/155#issuecomment-332282002).

And we will have validity check for dims for +- signs.

gfinak commented 6 years ago

So the idea is no more marker or channel info there? I'm fine with that. I think it will be easier to explain.

mikejiang commented 6 years ago

The changes have been pushed. The code involves the pop pattern is now cleaner than it used to be. Also - can allowed in dims in any circumstance since it no longer messes with pop in those refGate cases.

To turn off this validity check for the legacy template, simply set the global option, e.g.

opt <- getOption("openCyto")
opt[["check.pop"]] <- FALSE
options(openCyto = opt)