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Update parse_taxonomy.R #67

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adossantos1 wants to merge 1 commit into jbisanz:master from adossantos1:custom_parse_taxa

adossantos1 commented Jun 27, 2024 •

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Add option for adding custom ranks and trimming when importing taxa. Also add a warning when dropping ranks.
For phyloseq import use could be:

ps <- qiime2R::qza_to_phyloseq(features = features_path, tree = tree_path, metadata = metadata_path)
tax_table(ps) <- parse_taxonomy_custom(read_qza(taxonomy_path, tmp=tmp)$data) %>% as.matrix

For PR2 database with 9 ranks:

ps <- qiime2R::qza_to_phyloseq(features = features_path, tree = tree_path, metadata = metadata_path)
tax_table(ps) <- parse_taxonomy_custom(read_qza(taxonomy_path, tmp=tmp)$data, ranks = c("Domain", "Supergroup", "Division", "Subdivision", 
            "Class", "Order", "Family", "Genus", "Species")) %>% as.matrix

Fixes #66
Includes changes from bingli2019 and jthmiller pull requests


          Update parse_taxonomy.R

18b0f35

Custom ranks and trimming for parsing taxa

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