Modifying taxonomic annotation from RESCRIPt

[SoilRotifer (Mike Robeson)]

Hi @sln,

@sln

I have a small (!) concern regarding edit taxonomy.

Thank you for taking edit-taxonomy for a spin!

@sln

I am a bit scared to manually edit each single of them every single time I did a taxonomic assignment.

@sln

Do you think preparing a single search and replacement metadata file can be used in different projects or every time I got new data I should prepare a new metadata file to edit taxonomy?

I realized that I never explicitly stated the goal of edit-taxonomy. So, I added the following statement to the tutorial:

Typical use cases:

• Edit the taxonomy prior to generating a taxonomic classifier.
• Make taxonomy more "friendly" for plotting figures
  • Relabel non-official / un-accepted taxonomic labels, which are likely to cause confusion.
  • Truncate taxonomic names (e.g. based on a regular expression) so that the full lineage is not displayed in something like a heatmap.
• Or any other reasons we've not listed here.

If modifying the taxonomy for the first use case, there should be no need to edit the taxonomy each time you analyze your data. But it'd be a good idea to maintain / update your metadata file as you encounter additional mis-annotations. Then just use that whenever to make a classifier.