Nothing
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
refdb:::check_fields(x, c("sequence", "taxonomy")) x_seq <- x[[attributes(x)$refdb$sequence]]
Total number of sequences: r sum(!is.na(x_seq))
Number of unique sequences: r sum(!duplicated(x_seq[!is.na(x_seq)]))
refdb_plot_tax_barplot(x) refdb_plot_tax_treemap(x) if(all(c("latitude", "longitude") %in% names(refdb_get_fields(x, silent = TRUE))) ){ refdb_plot_map(x) }
check_typo <- refdb_check_tax_typo(x) check_typo <- dplyr::bind_rows(check_typo, .id = "Level") DT::datatable(check_typo, rownames = FALSE, options = list(searching = FALSE, pageLength = 10 ) )
check_taxo <- refdb_check_tax_conflict(x) check_taxo <- dplyr::bind_rows(check_taxo, .id = "Level") check_taxo <- dplyr::group_by(check_taxo, Level, Taxon) format_taxo <- function(y) { tax <- stringr::str_split(y, " > ") tax <- do.call("rbind", tax) tax_test <- apply(tax, 2, function(x) length(unique(x)) == 1) sel <- seq(min(which(tax_test == FALSE)) - 1, length(tax_test)) res <- apply(tax[, sel], 1, paste, collapse = " > ") if(min(sel) > 1) { res <- paste("... >", res) } res <- paste(res, collapse = "<br/>") return(res) } if(nrow(check_taxo) > 0) { check_taxo <- dplyr::summarise(check_taxo, Taxonomy = format_taxo(Taxonomy)) } DT::datatable(check_taxo, rownames = FALSE, escape = FALSE, options = list(searching = FALSE, pageLength = 10 ) )
check_seqs <- refdb_check_seq_conflict(x) if(nrow(check_seqs) == 0) { cat("No sequence conflict detected.") } else { check_seqs <- dplyr::group_by(check_seqs, level_conflict, sequence) check_seqs <- dplyr::summarise(check_seqs, taxonomy = format_taxo(taxonomy)) check_seqs <- dplyr::select(check_seqs, sequence, level_conflict, taxonomy) check_seqs$sequence <- paste('<span style="width: 250px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis; display:inline-block;">', check_seqs$sequence,'</span>') check_seqs <- setNames(check_seqs, c("Sequence", "Level", "Taxonomy")) DT::datatable(check_seqs, escape = FALSE, rownames = FALSE, options = list(searching = FALSE, pageLength = 10)) }
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