Commit 93850786 authored by Sandra Derozier's avatar Sandra Derozier
Browse files

Fix bug with filter when dplyr is not loaded

parent 024667b2
......@@ -43,14 +43,14 @@ sanitize_physeq_and_affi <- function(physeq, affi) {
old_to_new <- otu_dictionary %>% dplyr::select(-abundance) %>% tibble::deframe()
## Add abundance information to affiliation table
affi <- inner_join(otu_dictionary, affi, by = c("sequence" = "#observation_name")) %>%
affi <- dplyr::inner_join(otu_dictionary, affi, by = c("sequence" = "#observation_name")) %>%
tidyr::separate(blast_taxonomy, into = phyloseq::rank_names(physeq), sep = ";")
## Rename taxa in physeq object
phyloseq::taxa_names(physeq) <- old_to_new[phyloseq::taxa_names(physeq)] %>% unname()
## Remove previously curated taxa from affi
affi <- affi %>% filter(OTU %in% ambiguous_taxa(physeq))
affi <- affi %>% dplyr::filter(OTU %in% ambiguous_taxa(physeq))
list(
physeq = physeq,
......
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