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MHH-RCUG / haybaler

Haybaler: Collate/integrate reporting CSV or bam.txt files from the Wochenende pipeline https://github.com/MHH-RCUG/Wochenende
MIT License
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vegan ordination analysis #29

Open colindaven opened 3 years ago

colindaven commented 3 years ago

Hi @poer-sophia

analogously to our heatmaps in R, we might consider creating NMDS plots by default (if possible, not attempted, will only work if we don't need to provide too many parameters).

This package seems very nice for this task: google: vegan https://cran.r-project.org/web/packages/vegan/vignettes/intro-vegan.pdf

Perhaps we can try it in future.

Edit: Marie Pust and Ilona have suggested using MDS instead of PCA as the assumptions better reflect the data.

LisaHollstein commented 2 years ago

Is this still needed as well? Or is there any reason, why we shouldn't do this? I could use and integrate the MDS and/or PCA script Joël and I wrote.

colindaven commented 2 years ago

Sure, please test thoroughly first to see what already exists, and talk to Ilona as one of the main users to get her feedback. But yes, gladly.