#' @title Importing output pairwise orthologs tables generated with \code{\link{generate_ortholog_tables_all}}
#' @description Importing output pairwise orthologs tables generated with \code{\link{generate_ortholog_tables_all}}.
#' @param ortholog_tables_folder file path to output files generated with \code{\link{generate_ortholog_tables_all}}.
#' @author Hajk-Georg Drost
#' @export
import_ortholog_tables_all <- function(ortholog_tables_folder) {
if (!file.exists(ortholog_tables_folder))
stop("The folder '",ortholog_tables_folder, "' does not seem to exist. Please provide a valid folder path.", call. = FALSE)
message("Importing ortholog tab les generated with generate_ortholog_tables_all() from '", ortholog_tables_folder, " ...")
ortholog_tables <- file.path(ortholog_tables_folder, list.files(ortholog_tables_folder))
res <-
suppressMessages(dplyr::bind_rows(lapply(ortholog_tables, function(x)
readr::read_delim(
x,
col_names = TRUE,
delim = ";",
col_types = readr::cols(
"query_species" = readr::col_character(),
"subject_species" = readr::col_character(),
"query_id" = readr::col_character(),
"query_gene_locus_id" = readr::col_character(),
"subject_id" = readr::col_character(),
"subject_gene_locus_id" = readr::col_character(),
"dN" = readr::col_double(),
"dS" = readr::col_double(),
"dNdS" = readr::col_double(),
"evalue" = readr::col_double(),
"bit_score" = readr::col_double(),
"perc_identity" = readr::col_double(),
"num_ident_matches" = readr::col_double(),
"alig_length" = readr::col_integer(),
"mismatches" = readr::col_integer(),
"gap_openings" = readr::col_integer(),
"n_gaps" = readr::col_double(),
"pos_match" = readr::col_double(),
"ppos" = readr::col_double(),
"q_start" = readr::col_integer(),
"q_end" = readr::col_integer(),
"q_len" = readr::col_double(),
"qcov" = readr::col_double(),
"qcovhsp" = readr::col_double(),
"s_start" = readr::col_integer(),
"s_end" = readr::col_integer(),
"s_len" = readr::col_double(),
"score_raw" = readr::col_double()
)
))))
message("Import was successful!")
return(res)
}
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