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zhouhj1994 / LinDA

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Taxonomic name for ASVs #16

Open RachBioHaz opened 9 months ago

RachBioHaz commented 9 months ago

Hi, Thanks for creating this package. I've just started using LinDA and I'm not sure if the following is possible or already available.

1) I am using a phyloseq object that has a taxonomic table in it, is there a way to have the taxonomic name rather than the ASV listed in the output and plots? Or is there a method to edit individual plots after they're generated?

2) Also, is there a way to use the factors in the phyloseq object as the default order for reference level selection, or a manual way to set it?

Cheers

zhouhj1994 commented 8 months ago

Hi,

  1. The name listed in the output and plots is from the rowname of count table. Is it possible to match it with the taxonomic name? You can replace the rowname of the otu/count table with the taxonomic name before implementing linda.

  2. Currently, there is no an automatic way to select the level in linda. I guess one manual way is to merge/add the counts of otus belonging to the same level.

RachBioHaz commented 8 months ago

Thanks