R/read_enrich_tables.R

In isabellagrassucci/autoGO: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

#' @title Read enrichment results from tables
#'
#' @description Helper function to read all the enrichment results in order to proceed with the visualization in an automated way.
#' @param where_results Specify the folder in which you want to save the outputs. Default is "./". Note: if you are working with RNotebook the default working directory, if not specified, is the folder in which the .Rmd file is saved.
#' @param outfolder The name to assign to the folder for output saving. (Default = "results/"). NOTE: please add "/" at the end.
#' @param log2FC_threshold Threshold value for log2(Fold Change) for considering genes as differentially expressed (default = 0).
#' @param padj_threshold Threshold value for adjusted p-value significance (Defaults to 0.05).
#' @param which_list One of c("up_genes","down_genes","up_down_genes","everything"). Select a list of genes to perform the enrichment. Respectively, only up regulated genes (up_genes), only down regulated genes (down_genes), both up and down regulated genes (up_down_genes), or everything allow to load all the three kind of lists separately.
#' @param from_DE_analysis Default is TRUE, set to FALSE if the lists you want to upload are not from a differential expression analysis.
#' @param where_files Default is NULL, when from_DE_analysis = T it is mandatory to provide a path to specify where the list of genes are.
#' @param files_format Default is NULL, when from_DE_analysis = T it is mandatory to provide the extension of the list of genes you want to upload.
#' @export


read_enrich_tables <- function(where_results = "./", outfolder = "results/", log2FC_threshold = 0, padj_threshold = 0.05, which_list = c("up_genes","down_genes","up_down_genes","everything"), from_DE_analysis = T, where_files = NULL, files_format = NULL) {

  enrich_lists_path <- list.files(path = paste0(where_results,outfolder), recursive = T)
  enrich_lists_path <- paste0(where_results,outfolder,enrich_lists_path)
  enrich_lists_path <- enrich_lists_path[!grepl(pattern = ".xlsx", enrich_lists_path)]
  enrich_lists_path <- enrich_lists_path[grepl(pattern = "enrichment_tables", enrich_lists_path)]

  if (from_DE_analysis) {
    to_read <- enrich_lists_path[grepl(pattern = paste0("thFC",log2FC_threshold,"_thPval",padj_threshold), enrich_lists_path)]
  } else if (!from_DE_analysis) {
    if (is.null(where_files)) stop("Required parameter: 'where_files' for path of enrichment tables.")
    if (is.null(files_format)) stop("Required parameter: 'files_format' for extension of enrichment tables, should be like '.txt' or '.tsv', etc.")
    enrich_lists_path <- list.files(path = where_files, pattern = files_format, recursive = T)
    enrich_lists_path <- paste0(where_files,enrich_lists_path)
    to_read <- enrich_lists_path
    which_list <- "everything"
  }

  if (which_list == "up_down_genes") {
    to_read <- to_read[grepl(pattern = "up_down_genes", to_read)]
  } else if (which_list == "up_genes") {
    to_read <- to_read[grepl(pattern = "up_genes", to_read)]
  } else if (which_list == "down_genes") {
    to_read <- to_read[grepl(pattern = "/down_genes", to_read)]
  } else if (which_list == "everything") {
    to_read <- to_read
  }

  readed <- lapply(to_read, function (x) read_tsv(x, col_types = cols()))
  names(readed) <- gsub(".tsv", "",to_read)

  return(readed)
}