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I am quite new to d3 and I am trying to make a choropleth map of the US. But my point is how to adjust Alaska and Hawaii in the final map.

In the past I used to do this in Illustrator, but I am not sure how to do this in d3.

Do I need to make these changes first in QGIS and then convert my data sets to TopoJSON?

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    Have a look for the D3 "AlbersUSA" projection. Or look at using Alaska and Hawaii inset maps overlaid on the main USA map. – user2856 Mar 27 at 23:09
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As user2856 pointed out in the comment:

You can just use the d3.geoAlbersUsa() projection and it will show Alaska and Hawaii on the bottom left.

Take a look here for an explanation: https://github.com/d3/d3-geo#geoAlbersUsa

And an example here: https://bl.ocks.org/mbostock/4090848

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