The brush function in d3 is great and simple to use. However, for a complex graph like a force-directed tree and scatter plot graph, more flexible selection of nodes may be necessary to understand the property of a particular region.
Is there any way to implement such kind of selection in D3?
There is a D3 plugin called lasso.js which seems to provide the functionality you are looking for. The example looks like the graphic you attached to your post.
Another one worth a look is the Polybrush plugin which provides a polygon selection. This, however, might be to restrictive for your needs.
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