To explore the potential for batch effects, we can make UMAPs colored by histology and shaped by sequencing center. We can do this twice: once for all histologies, and once only for histologies that are shared among centers. These may be helpful supplementary figure panels (there's lots of room in S5!) to clarify that we do not anticipate major batch effects across centers.
Related to https://github.com/AlexsLemonade/OpenPBTA-manuscript/issues/366
To explore the potential for batch effects, we can make UMAPs colored by histology and shaped by sequencing center. We can do this twice: once for all histologies, and once only for histologies that are shared among centers. These may be helpful supplementary figure panels (there's lots of room in S5!) to clarify that we do not anticipate major batch effects across centers.