Returns the ggplot2 objects in the function maaslin_plot_results

biobakery · Nov 26, 2024 · a9fdd36 · a9fdd36
1 parent 98b31a8
commit a9fdd36
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/R/maaslin3.R b/R/maaslin3.R
@@ -2326,6 +2326,7 @@ maaslin_plot_results <- function(output,
                                 plot_associations = TRUE,
                                 max_pngs = 30,
                                 balanced = FALSE) {
+    ret_plots <- list()
     # create an output folder and figures folder if it does not exist
     if (!file.exists(output)) {
         logging::loginfo("Creating output folder")
@@ -2363,7 +2364,7 @@ maaslin_plot_results <- function(output,
             heatmap_vars <- trimws(unlist(strsplit(heatmap_vars, ',')))
         }
 
-        maaslin3_summary_plot(
+        sum_plot <- maaslin3_summary_plot(
             merged_results,
             summary_plot_file,
             figures_folder,
@@ -2376,7 +2377,7 @@ maaslin_plot_results <- function(output,
             balanced = balanced
         )
     }
-
+    ret_plots[["Summary_plot"]] <- sum_plot
     # Individual association plots
     if (plot_associations) {
         logging::loginfo(
@@ -2410,9 +2411,9 @@ maaslin_plot_results <- function(output,
                 invokeRestart("muffleWarning")
             })
         })
-
-        return(plots_out)
+        ret_plots[["Assocations"]] <- plots_out
     }
+    return(ret_plots)
 }
 
 maaslin_plot_results_from_output <- function(output,

diff --git a/R/viz.R b/R/viz.R
@@ -473,6 +473,7 @@ maaslin3_summary_plot <-
             median_comparison_abundance = FALSE,
             median_comparison_prevalence = FALSE,
             balanced=FALSE) {
+        ret_plots <- list()
         if (first_n > 200) {
             logging::logerror(
                 paste(
@@ -686,6 +687,9 @@ maaslin3_summary_plot <-
         } else {
             final_plot <- NULL
         }
+        ret_plots[["coefficient"]] <- p1
+        ret_plots[["heat"]] <- p2
+        ret_plots[["final"]] <- final_plot
 
         # Save plot
         if (!is.null(final_plot)) {
@@ -731,6 +735,7 @@ maaslin3_summary_plot <-
                 })
             })
         }
+        return(ret_plots)
     }
 
 # Create a scatterplot for abundance vs. continuous associations