R/load_kegg_annotations.R

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

#' Create a data frame of pathways to gene IDs from KEGGREST
#'
#' This seeks to take the peculiar format from KEGGREST for pathway<->genes and
#' make it easier to deal with.
#'
#' @param species  String to use to query KEGG abbreviation.
#' @param abbreviation  If you already know the abbreviation, use it.
#' @param flatten  Flatten nested tables?
#' @return  dataframe with rows of KEGG gene IDs and columns of NCBI gene IDs
#'  and KEGG paths.
#' @author atb
#' @export
load_kegg_annotations <- function(gene_table, species = "coli",
                                  abbreviation = NULL, flatten = TRUE) {
  chosen <- NULL
  if (!is.null(abbreviation)) {
    species <- NULL
  }
  if (is.null(abbreviation) & is.null(species)) {
    stop("This requires either a species or 3 letter kegg id.")
  } else if (!is.null(abbreviation)) {
    chosen <- abbreviation
  } else {
    ## Then the species was provided.
    abbreviation <- get_kegg_orgn(species)
    if (length(abbreviation) == 0) {
      stop("Unable to find a matching abbreviation for the search: ", species, ".")
    }
    message("The possible abbreviations are: ", toString(abbreviation), ".")
    message("Choosing the first one: ", abbreviation[[1]])
    chosen <- abbreviation[[1]]
  }

  ## Now that we have an abbreviation, we should be able to gather some information from keggrest.
  genes_df <- data.frame("ncbi_geneid" = "undef", "GID" = "undef")
  genes_vector <- try(KEGGREST::keggConv("ncbi-geneid", chosen), silent = TRUE)
  if (! "try-error" %in% class(genes_vector)) {
    genes_df <- kegg_vector_to_df(genes_vector, final_colname = "ncbi_geneid", flatten = flatten)
  }

  prot_df <- data.frame("ncbi-proteinid" = "undef", "GID" = "undef")
  prot_vector <- try(KEGGREST::keggConv("ncbi-proteinid", chosen), silent = TRUE)
  if (! "try-error" %in% class(prot_vector)) {
    prot_df <- kegg_vector_to_df(prot_vector, final_colname = "ncbi_proteinid", flatten = flatten)
  }

  uniprot_df <- data.frame("uniprotid" = "undef", "GID" = "undef")
  uniprot_vector <- try(KEGGREST::keggConv("uniprot", chosen), silent = TRUE)
  if (! "try-error" %in% class(uniprot_vector)) {
    uniprot_df <- kegg_vector_to_df(uniprot_vector, final_colname = "uniprotid", flatten = flatten)
  }

  path_df <- data.frame("pathways" = "undef", "GID" = "undef")
  path_vector <- try(KEGGREST::keggLink("pathway", chosen), silent = TRUE)
  if (! "try-error" %in% class(path_vector)) {
    path_df <- kegg_vector_to_df(path_vector, final_colname = "pathways", flatten = flatten)
  }

  if (isTRUE(flatten)) {
    result <- merge(genes_df, prot_df, by = "GID", all = TRUE)
    rownames(result) <- result[["ID"]]
    result <- merge(result, uniprot_df, by = "GID", all = TRUE)
    rownames(result) <- result[["ID"]]
    result <- merge(result, path_df, by = "GID", all = TRUE)
    rownames(result) <- result[["ID"]]
  } else {
    result <- merge(genes_df, prot_df, by = "GID", all = TRUE)
    result <- merge(result, uniprot_df, by = "GID", all = TRUE)
    result <- merge(result, path_df, by = "GID", all = TRUE)
  }
  drop_idx <- result[["GID"]] == "undef"
  result <- result[!drop_idx, ]

  ## Clean up the various IDs so they are recognizable.
  result[["ncbi_geneid"]] <- gsub(
    pattern = "ncbi-geneid:", replacement = "", x = result[["ncbi_geneid"]])
  result[["ncbi_proteinid"]] <- gsub(
    pattern = "ncbi-proteinid:", replacement = "", x = result[["ncbi_proteinid"]])
  result[["uniprotid"]] <- gsub(pattern = "up:", replacement = "", x = result[["uniprotid"]])
  result[["pathways"]] <- gsub(pattern = "path:", replacement = "", x = result[["pathways"]])
  result[["kegg_geneid"]] <- glue::glue("{chosen}:{result[['GID']]}")
  ## Now we have a data frame of all genes <-> ncbi-ids, pathways
  result_nas <- is.na(result)
  result[result_nas] <- ""

  ## Now lets use the uniprot_xref column to fix the rownames
  gene_table[["KEGG_GID"]] <- gsub(x = toupper(gene_table[["GID"]]),
                                   pattern = "\\.", replacement = "_")
  gene_table <- gene_table[, c("GID", "KEGG_GID")]
  result_merged <- merge(gene_table, result, by.x = "KEGG_GID", by.y = "GID")
  GID <- NULL
  result <- result_merged %>%
    relocate(GID)
  message("Returning KEGGREST annotations.")
  return(result)
}