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I use the Atlas of QGIS 3.2. I already figured out how to show only attributes inside current Atlas feature using $id = @atlas_featureid.

My problem is, as a coverage layer I am using layer with municipality borders, although my featured layer has borders of smaller administrative units. When I use the $id = @atlas_featureid, Atlas only shows one diagram per Map.

I partially found a solution to hide diagrams outside current map feature in this thread, but it doesn't solve my problem.

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If you want to show all the features that fall within your atlas feature then you want an expression like:

contains(  @atlas_geometry , $geometry )

that will select all of the features who's geometry falls within the atlas feature's geometry.

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