Update ggpicrust2.R

cafferychen777 · Nov 4, 2023 · b4abba0 · b4abba0
1 parent 2184a69
commit b4abba0
Showing 1 changed file with 13 additions and 13 deletions.
diff --git a/R/ggpicrust2.R b/R/ggpicrust2.R
@@ -108,17 +108,17 @@ ggpicrust2 <- function(file = NULL,
   # Create an empty list
   plot_result_list <- list()
 
-  cat("Starting the ggpicrust2 analysis...\n")
+  message("Starting the ggpicrust2 analysis...\n")
 
   if (ko_to_kegg == TRUE){
-    cat("Converting KO to KEGG...\n")
+    message("Converting KO to KEGG...\n")
     plot_result_list <- list()
     abundance <- if (!is.null(file)) {
       ko2kegg_abundance(file)
     } else {
       ko2kegg_abundance(data = data)
     }
-    cat("Performing pathway differential abundance analysis...\n")
+    message("Performing pathway differential abundance analysis...\n")
     daa_results_df <- pathway_daa(
       abundance = abundance,
       metadata = metadata,
@@ -142,11 +142,11 @@ ggpicrust2 <- function(file = NULL,
       message(paste("Success: Found", num_significant_biomarkers, "statistically significant biomarker(s) in the dataset."))
     }
 
-    cat("Annotating pathways...\n")
+    message("Annotating pathways...\n")
     daa_results_df  <-
       pathway_annotation(daa_results_df = daa_results_df, ko_to_kegg = TRUE)
     j <- 1
-    cat("Creating pathway error bar plots...\n")
+    message("Creating pathway error bar plots...\n")
     for (i in unique(daa_results_df$method)) {
       daa_sub_method_results_df <-
         daa_results_df[daa_results_df[, "method"] == i, ]
@@ -167,13 +167,13 @@ ggpicrust2 <- function(file = NULL,
         list(plot = combination_bar_plot, results = daa_sub_method_results_df)
       # Add sublists to the main list
       plot_result_list[[j]] <- sub_list
-      cat(sprintf("Plot %d created.\n", j))
+      message(sprintf("Plot %d created.\n", j))
       j <- j + 1
     }
-    cat("ggpicrust2 analysis completed.\n")
+    message("ggpicrust2 analysis completed.\n")
     return(plot_result_list)
   } else {
-    cat("Reading input file or using provided data...\n")
+    message("Reading input file or using provided data...\n")
     plot_result_list <- list()
     abundance <- if (!is.null(file)) {
       readr::read_delim(
@@ -188,7 +188,7 @@ ggpicrust2 <- function(file = NULL,
     abundance <- as.data.frame(abundance)
     rownames(abundance) <- abundance[, 1]
     abundance <- abundance[, -1]
-    cat("Performing pathway differential abundance analysis...\n")
+    message("Performing pathway differential abundance analysis...\n")
     daa_results_df <- pathway_daa(
       abundance = abundance,
       metadata = metadata,
@@ -201,15 +201,15 @@ ggpicrust2 <- function(file = NULL,
     if(daa_method == "Lefse") {
       stop("The 'Lefse' method is not suitable for the ggpicrust2() function as Lefse in R does not output p-values, only effect sizes.")
     }
-    cat("Annotating pathways...\n")
+    message("Annotating pathways...\n")
     daa_results_df <-
       pathway_annotation(
         pathway = pathway,
         ko_to_kegg = ko_to_kegg,
         daa_results_df = daa_results_df
       )
     j <- 1
-    cat("Creating pathway error bar plots...\n")
+    message("Creating pathway error bar plots...\n")
     for (i in unique(daa_results_df$method)) {
       daa_sub_method_results_df <-
         daa_results_df[daa_results_df[, "method"] == i, ]
@@ -230,10 +230,10 @@ ggpicrust2 <- function(file = NULL,
         list(plot = combination_bar_plot, results = daa_sub_method_results_df)
       # Add sublists to the main list
       plot_result_list[[j]] <- sub_list
-      cat(sprintf("Plot %d created.\n", j))
+      message(sprintf("Plot %d created.\n", j))
       j <- j + 1
     }
-    cat("ggpicrust2 analysis completed.\n")
+    message("ggpicrust2 analysis completed.\n")
     return(plot_result_list)
   }