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It has been mentioned in the vignette of dendextend R package:

It is also worth noting that some order are impossible to achieve for a given tree’s topology. In such cases, the function will do its “best” to get as close as possible to the requested rotation.

I wonder if that is possible to retrieve the final order of the branches after rotating given I supplied some "impossible order"?

I am going to reorder a dendrogram with more than 20000 nodes (from WGCNA output), I found that genes were not clustered together while I believe it can be solved by rotating the branches.

MrFlick
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William Wong
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    It's easier to help you if you provide a [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) with sample input and desired output that can be used to test and verify possible solutions. – MrFlick May 04 '22 at 15:57

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