Fix/lowdepth sample fix#8
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miraep8
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Sep 17, 2025
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Looks good to me - thanks for adding the test cases as well!
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| get_metaphlan_analyses <- function(con, analysis_ids, schema="public") { | ||
| raw_results <- get_subset_pg_df("mgx_metaphlan", "ia_id", analysis_ids, schema=schema) %>% | ||
| get_metaphlan_analyses <- function(con, analysis_ids, schema="public", include_failures=FALSE) { |
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Nice, I think this include_failures flag is a good way to give people the data for all the samples they sequenced if they really want it! 👍
| if (include_failures){ | ||
| if (sum(raw_results[raw_results$clade_name == "unclassified", "estimated_number_of_reads_from_the_clade"]) > 0){ | ||
| print(raw_results[raw_results$clade_name== "unclassified", "ia_id"]) | ||
| stop("some of the above analyses have metaphlan failures where estimated_number of reads from the clade is not zero as expected; please alert of the vdbR delevopers that the metaphlan output has changed") |
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Nice! Hopefully a good catch
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This addresses how we consider the (usually poor quality) samples that have no metaphlan hits in the context of creating phyloseq objects. vdbR now will error and tell the user which samples they should remove from their metadata. Making this a hard error rather than a warning should clarify to users which samples they need to be aware of.