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solgenomics / sgn

The code behind the Sol Genomics Network, Cassavabase and other Breedbase websites
https://solgenomics.net
MIT License
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Creating AMMI plot based index #4420

Open pa279 opened 1 year ago

pa279 commented 1 year ago

Expected Behavior

The AMMI analysis is based on a single trait. However, it will be nice to see how we can store the selection index of a trial and use it for AMMI. Let's assume we have an MLT trial across 7 locations and phenotyped for 10 traits. We can have an index value for each genotype across the 7 locations. Only the location becomes a factor here with a single index.

https://tiagoolivoto.github.io/metan/

For Bugs:

Environment

Steps to Reproduce

chris263 commented 1 year ago

I would suggest allow create datasets using index besides traits.

lukasmueller commented 1 year ago

Is the selection index a simple post-calculation or is this somehow baked into the AMMI analysis?

chris263 commented 1 year ago

The idea is first calculate the selection index. Then, store the index as a trait. In this way will be possible to create datasets with indices allowing many analysis tools to use it (including AMMI, mixed models, heritability...)

lukasmueller commented 1 year ago

With the Selection Index tool, you can already generate a selection index and store it in the database. It can be re-used in other tools, such as it is done in the GCPC tool. Would that be a possible model for the AMMI tool?

chris263 commented 1 year ago

I've to find a way to include index with datasets. I'll check GCPC. Then, it will be possible to be included in AMMI.