search

RGLab / flowIncubator

Routines that don't belong to the core flow packages yet.
1 stars 3 forks source link

Supporting CytoBank's gates visible in "Working Illustration" view but not captured in GatingML #25

Open ptvan opened 8 years ago

ptvan commented 8 years ago

In CytoBank (premium version as of July 7th, 2016), users can arbitrarily overlay gates defined in an experiment on any population, even if these gates are not defined under those populations and are not captured in gatingML when CytoBank exports the experiment. example

In the example above, IL-10+ is only defined for the Non Naive B cells population, and this is exported in the gatingML and imported into OpenCyto. However, in CytoBank, user can choose to overlay IL-10+ on Naive B cells, Unswitched B (or any other population), plot these gates with IL-10+ overlaid, and calculate cell proportions. This is accomplished in CytoBank's "Working Illustration" function: Show Table of Statistics -> Gate: <choose IL-10+> (NOT available in CytoBank community version)

Until we have a way to capture this Working Illustration view from CytoBank, for compatibility, OpenCyto users will have to manually create these additional implied gates (Naive B cells/IL-10+, Unswitched B/IL-10+, etc...) after asking the CytoBank user which gate was the "original" that is represented in the GatingML (there may be >1 per experiment...).

ptvan commented 8 years ago

As @mikejiang discovered, it's rather straightforward for CytoBank users to copy gates en masse in the Population Manager and re-export the GatingML. I'm closing this issue as a result, though we could reopen it if in the future there is something else about Working Illustration view we want to import/capture

ptvan commented 8 years ago

Reopening this issue. As noted above, CytoBank users can copy gates en masse. However, currently (July 8th, 2016), the additional gates caused CytoBank Premium to become very slow, sometimes even crashing the page (at least on Firefox on Ubuntu). So copying gates may not be a viable option for CytoBank users, and we may want to support importing/reading the Working Illustrationview