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Mapbox: is it possible to update layer hierarchy?

I have a Mapbox with my own layers, says labels of towns and landmarks...

say I want to highlight one specific landmark and I want to move its z-index higher because otherwise, it would overlap with some other elements...

Can I use map.setLayoutProperty or is there anything else that I can do?

If I got your question correctly, you're looking for a way to change z-index of some layer above another layer. ( not some feature above another feature). Here it the way:

https://www.mapbox.com/mapbox-gl-js/api/#map#movelayer

map.moveLayer(yourLandmarkLayerId, someAnotheLayerId);

If you would like just to move landmark layer to top of layer hierarchy:

map.moveLayer(yourLandmarkLayerId);

PS For moving layer, you should know it's ID:

var layers = map.getStyle().layers;
var layerId = layers[i].id;

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