Starting 6.0 it is encouraged to use different indexes for different types/formats of data. But I don't see a way to provide multiple indexes pattern (say user-,tweets-) in kibana for a single visualization. Such indexes pattern is very well supported by ElasticSearch. I have some 100s of monthly index patterns and visualization can be done on two or more combinations of index patterns.
there are currently only a limited amount of chart types, that can handle multiple index patterns in one chart. Mainly you can use the Visual Builder and/or Timelion.
We are also working on a new editor and rendering pipeline which will hopefully solve that problem in the long run for all chart types.
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