R/print.R

In GuangchuangYu/DOSE: Disease Ontology Semantic and Enrichment analysis

##' show method for \code{gseaResult} instance
##'
##' @name show
##' @docType methods
##' @rdname show-methods
##'
##' @title show method
##' @return message
##' @importFrom methods show
##' @exportMethod show
##' @usage show(object)
##' @author Guangchuang Yu \url{https://yulab-smu.top}
setMethod("show", signature(object="gseaResult"),
          function (object){
              params <- object@params
              cat("#\n# Gene Set Enrichment Analysis\n#\n")
              cat("#...@organism", "\t", object@organism, "\n")
              cat("#...@setType", "\t", object@setType, "\n")
              kt <- object@keytype
              if (kt != "UNKNOWN") {
                  cat("#...@keytype", "\t", kt, "\n")
              }

              cat("#...@geneList", "\t")
              str(object@geneList)
              cat("#...nPerm", "\t", params$nPerm, "\n")
              cat("#...pvalues adjusted by", paste0("'", params$pAdjustMethod, "'"),
                  paste0("with cutoff <", params$pvalueCutoff), "\n")
              cat(paste0("#...", nrow(object@result)), "enriched terms found\n")
              str(object@result)
              cat("#...Citation\n")
              if (object@setType == "DO" || object@setType == "DOLite" || object@setType == "NCG") {
                  citation_msg <- paste("  Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an",
                                    "  R/Bioconductor package for Disease Ontology Semantic and Enrichment",
                                    "  analysis. Bioinformatics 2015, 31(4):608-609", sep="\n", collapse="\n")
              } else if (object@setType == "Reactome") {
                  citation_msg <- paste("  Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for",
                                        "  reactome pathway analysis and visualization. Molecular BioSystems",
                                        "  2016, 12(2):477-479", sep="\n", collapse="\n")
              } else {
                  citation_msg <- paste(" T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.", 
                                        " clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.", 
                                        " The Innovation. 2021, 2(3):100141", sep="\n", collapse="\n")
              }
              cat(citation_msg, "\n\n")
          }
          )

##' show method for \code{enrichResult} instance
##'
##' @name show
##' @docType methods
##' @rdname show-methods
##'
##' @title show method
##' @param object A \code{enrichResult} instance.
##' @return message
##' @importFrom utils str
##' @importFrom methods show
##' @exportMethod show
##' @usage show(object)
##' @author Guangchuang Yu \url{https://yulab-smu.top}
setMethod("show", signature(object="enrichResult"),
          function (object){
              cat("#\n# over-representation test\n#\n")
              cat("#...@organism", "\t", object@organism, "\n")
              cat("#...@ontology", "\t", object@ontology, "\n")
              kt <- object@keytype
              if (kt != "UNKNOWN") {
                  cat("#...@keytype", "\t", kt, "\n")
              }
              cat("#...@gene", "\t")
              str(object@gene)
              cat("#...pvalues adjusted by", paste0("'", object@pAdjustMethod, "'"),
                  paste0("with cutoff <", object@pvalueCutoff), "\n")
              object <- get_enriched(object)
              n <- nrow(object@result)
              cat(paste0("#...", n), "enriched terms found\n")
              if (n > 0) str(object@result)
              cat("#...Citation\n")
              if (object@ontology == "DO" || object@ontology == "DOLite" || object@ontology == "NCG") {
                  citation_msg <- paste("  Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an",
                                    "  R/Bioconductor package for Disease Ontology Semantic and Enrichment",
                                    "  analysis. Bioinformatics 2015, 31(4):608-609", sep="\n", collapse="\n")
              } else if (object@ontology == "Reactome") {
                  citation_msg <- paste("  Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for",
                                        "  reactome pathway analysis and visualization. Molecular BioSystems",
                                        "  2016, 12(2):477-479", sep="\n", collapse="\n")
              } else if (object@ontology == "MeSH") {
                  citation_msg <- paste(" Guangchuang Yu.",
                             " Using meshes for MeSH term enrichment and semantic analyses.",
                             " Bioinformatics 2018, 34(21):3766-3767", sep="\n", collapse="\n")
                
              } else {
                  citation_msg <- paste(" T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.", 
                                        " clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.", 
                                        " The Innovation. 2021, 2(3):100141", sep="\n", collapse="\n")
              }
              cat(citation_msg, "\n\n")
          })