R/dplyr-pathway_database.R

In tidymass/metpath: Pathway analysis for metabolomics data

#' @method filter pathway_database
#' @docType methods
#' @importFrom rlang quos !!!
#' @importFrom dplyr filter
#' @export
filter.pathway_database <-
  function(.data, ..., .preserve = FALSE) {
    dots <- quos(...)
    # browser()
    if (length(.data@gene_list) == 0) {
      .data@gene_list = vector(mode = "list",
                               length = length(.data@pathway_id)) %>%
        purrr::map(function(x) {
          x = data.frame()
          x
        })
    }
    
    if (length(.data@compound_list) == 0) {
      .data@compound_list = vector(mode = "list",
                                   length = length(.data@pathway_id)) %>%
        purrr::map(function(x) {
          x = data.frame()
          x
        })
    }
    
    if (length(.data@protein_list) == 0) {
      .data@protein_list = vector(mode = "list",
                                  length = length(.data@pathway_id)) %>%
        purrr::map(function(x) {
          x = data.frame()
          x
        })
    }
    
    describtion = .data@describtion
    describtion =
      describtion %>%
      purrr::map(function(x) {
        x = paste(x, collapse = ";")
        if (is.null(x)) {
          return("")
        } else{
          x
        }
      }) %>%
      unlist
    
    pathway_class = .data@pathway_class
    pathway_class =
      pathway_class %>%
      purrr::map(function(x) {
        x = paste(x, collapse = ";")
        if (is.null(x)) {
          return("")
        } else{
          x
        }
      }) %>%
      unlist
    
    gene_list = .data@gene_list
    gene_number =
      gene_list %>%
      lapply(nrow) %>%
      unlist()
    
    compound_list = .data@compound_list
    compound_number =
      compound_list %>%
      lapply(nrow) %>%
      unlist()
    
    protein_list = .data@protein_list
    protein_number =
      protein_list %>%
      lapply(nrow) %>%
      unlist()
    
    if (is.null(protein_number)) {
      protein_number = rep(0, length(.data@pathway_id))
    }
    
    temp_data =
      data.frame(
        pathway_id = .data@pathway_id,
        pathway_name = .data@pathway_name,
        describtion,
        pathway_class,
        gene_number,
        compound_number,
        protein_number
      )
    
    temp_data =
      dplyr::filter(temp_data, !!!dots, .preserve = .preserve)
    
    idx =
      match(temp_data$pathway_id, .data@pathway_id)
    
    .data@pathway_id = .data@pathway_id[idx]
    .data@pathway_name = .data@pathway_name[idx]
    .data@describtion = .data@describtion[idx]
    .data@pathway_class = .data@pathway_class[idx]
    .data@gene_list = .data@gene_list[idx]
    .data@compound_list = .data@compound_list[idx]
    .data@protein_list = .data@protein_list[idx]
    .data@reference_list = .data@reference_list[idx]
    .data@related_disease = .data@related_disease[idx]
    .data@related_module = .data@related_module[idx]
    
    return(.data)
  }

#' @importFrom dplyr filter
#' @export
dplyr::filter