update the print function in each class

R/trans_abund.R

@@ -892,7 +892,7 @@ trans_abund <- R6Class(classname = "trans_abund",
 			}
 			invisible(self)
 		}
-		),
+	),
 	private = list(
 		adjust_axis_facet = function(plot_data, x_axis_name, order_x){
 			# order x axis samples and facet

R/trans_diff.R

@@ -1580,16 +1580,8 @@ trans_diff <- R6Class(classname = "trans_diff",
 			}
 			tree <- tree + theme(legend.position = "right", legend.title = element_blank())
 			tree
-		},
-		#' @description
-		#' Print the trans_alpha object.
-		print = function() {
-			cat("trans_diff object:\n")
-			cat(paste("res_diff have", ncol(self$res_diff), "columns: ", paste0(colnames(self$res_diff), collapse = ", "), "\n"))
-			if(!is.null(self$res_abund)) cat(paste("res_abund have", ncol(self$res_abund), "columns: ", paste0(colnames(self$res_abund), collapse = ", "), "\n"))
-			invisible(self)
 		}
-		),
+	),
 	private = list(
 		check_taxa_level_all = function(taxa_level){
 			if(taxa_level == "all"){

R/trans_env.R

@@ -1468,6 +1468,7 @@ trans_env <- R6Class(classname = "trans_env",
 			}else{
 				cat("No environmental variable table stored in the object.\n")
 			}
+			invisible(self)
 		}
 	),
 	private = list(

R/trans_func.R

@@ -835,24 +835,6 @@ trans_func <- R6Class(classname = "trans_func",
 			self$res_tax4fun2_rFRI <- rel_functional_redundancy_final
 			message('Relative functional redundancy is stored in object$res_tax4fun2_rFRI')
 			invisible(self)
-		},
-		#' @description
-		#' Print the trans_func object.
-		print = function(){
-			cat("trans_func object:\n")
-			cat(paste("Functional analysis for", self$for_what, ".\n"))
-			if(!is.null(self$sample_table)){
-				cat("sample_table is available.\n")
-			}
-			if(!is.null(self$otu_table)){
-				cat("otu_table is available.\n")
-			}
-			if(!is.null(self$tax_table)){
-				cat("tax_table is available.\n")
-			}
-			if(!is.null(self$rep_fasta)){
-				cat("rep_fasta is available.\n")
-			}
 		}
 	),
 	active = list(

R/trans_network.R

@@ -1251,7 +1251,7 @@ trans_network <- R6Class(classname = "trans_network",
 			}
 			invisible(self)
 		}
-		),
+	),
 	private = list(
 		check_filter_number = function(input, param = "filter_thres"){
 			if(nrow(input) == 0){

R/trans_venn.R

@@ -542,8 +542,9 @@ trans_venn <- R6Class(classname = "trans_venn",
 		#' Print the trans_venn object.
 		print = function() {
 			print(self$data_summary)
+			invisible(self)
 		}
-		),
+	),
 	private = list(
 		# modified from vennSets function in systemPipeR package
 		vennSets = function(setmatrix, allcombl, index, setunion){