Add 'render' function to bypass plot generation

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MetaVolcanoR
 Type: Package
 Title: Gene Expression Meta-analysis Visualization Tool
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(person("Cesar", "Prada", email = "cesar.prada@usp.br", 
     role = c("aut", "cre")), person("Diogenes", "Lima", email = "diogenes.lima@usp.br", 
     role = c("aut")), person("Helder", "Nakaya", email = "hnkaya@usp.br",
@@ -39,4 +39,4 @@ biocViews: GeneExpression, DifferentialExpression, Transcriptomics, mRNAMicroarr
 LazyData: true
 roxygennote: 6.1.1.9000
 VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.3

NAMESPACE

@@ -15,19 +15,21 @@ export(remodel)
 export(rename_col)
 export(set_degbar_data)
 export(votecount_mv)
+import(dplyr)
 import(ggplot2)
-import(data.table)
-import(graphics)
-import(stats)
-import(tidyr)
-importFrom(grDevices, pdf, dev.off)
-importFrom(htmlwidgets, saveWidget)
 importFrom(cowplot,plot_grid)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,pdf)
+importFrom(graphics,plot)
+importFrom(htmlwidgets,saveWidget)
 importFrom(methods,'slot<-')
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,show)
 importFrom(parallel,mclapply)
-importFrom(plotly, as_widget, ggplotly)
+importFrom(plotly,as_widget)
+importFrom(plotly,ggplotly)
+importFrom(stats,median)
+importFrom(stats,quantile)
+importFrom(stats,setNames)
 importFrom(topconfects,normal_confects)
-importFrom(dplyr, mutate, arrange, select, matches, '%>%')

R/combining_mv.R

@@ -25,6 +25,11 @@ NULL
 #' @param outputfolder /path where to write the results/
 #' @param draw wheather or not to draw the .pdf or .html visualization 
 #'        <c(NULL, "PDF", "HTML")>
+#' @param render A boolean parameter that determines whether the plot should be rendered. 
+#' If `TRUE`, the function will produce and save the plot based on the specified `draw` 
+#' parameter (either as an HTML or PDF file). If `FALSE` (default), no plot will be 
+#' rendered or saved. It's useful for cases where you might want to run the function 
+#' for its side effects or calculations without necessarily visualizing the result.
 #' @return \code{MetaVolcano} object
 #' @keywords write 'combining meta-analysis' metavolcano
 #' @export
@@ -36,7 +41,7 @@ combining_mv <- function(diffexp=list(), pcriteria="pvalue",
 			 foldchangecol="Log2FC", genenamecol="Symbol", 
 			 geneidcol=NULL, metafc="Mean", metathr=0.01, 
 			 collaps="FALSE", jobname="MetaVolcano", 
-			 outputfolder=".", draw="HTML") {
+			 outputfolder=".", draw="HTML", render = F) {
 
     if(!draw %in% c('PDF', 'HTML')) {
 
@@ -159,24 +164,25 @@ combining_mv <- function(diffexp=list(), pcriteria="pvalue",
 
     # --- Drawing combining MetaVolcano
     gg <- plot_mv(meta_diffexp, NULL, genecol, TRUE, metafc)
-
-    if(draw == "HTML") {
-
-        # --- Writing html device for offline visualization
-        saveWidget(as_widget(ggplotly(gg)), 
-            paste0(normalizePath(outputfolder), 
-	        '/combining_method_MetaVolcano_', jobname, ".html"))
-
-    } else if(draw == "PDF") {
-
-        # --- Writing PDF visualization
-        pdf(paste0(normalizePath(outputfolder), 
-            '/combining_method_MetaVolcano_', jobname, ".pdf"), 
-	     width = 4, height = 5)
-	        plot(gg)
-        dev.off()
-
-    } 
+    if(render) {
+      if(draw == "HTML") {
+
+          # --- Writing html device for offline visualization
+          saveWidget(as_widget(ggplotly(gg)), 
+              paste0(normalizePath(outputfolder), 
+  	        '/combining_method_MetaVolcano_', jobname, ".html"))
+
+      } else if(draw == "PDF") {
+
+          # --- Writing PDF visualization
+          pdf(paste0(normalizePath(outputfolder), 
+              '/combining_method_MetaVolcano_', jobname, ".pdf"), 
+  	     width = 4, height = 5)
+  	        plot(gg)
+          dev.off()
+
+      } 
+    }
 
     # Set combining result
     icols <- paste(c(genecol, pcriteria, foldchangecol), collapse="|")

R/rem_mv.R

@@ -47,6 +47,11 @@ setClass('MetaVolcano', slots = list(input='data.frame',
 #' @param outputfolder /path where to write the results/
 #' @param draw wheather or not to draw the .html visualization <logical>
 #' @param ncores the number of processors the user wants to use <integer>
+#' #' @param render A boolean parameter that determines whether the plot should be rendered. 
+#' If `TRUE`, the function will produce and save the plot based on the specified `draw` 
+#' parameter (either as an HTML or PDF file). If `FALSE` (default), no plot will be 
+#' rendered or saved. It's useful for cases where you might want to run the function 
+#' for its side effects or calculations without necessarily visualizing the result.
 #' @keywords write 'combining meta-analysis' metavolcano
 #' @return MetaVolcano object
 #' @export
@@ -61,7 +66,7 @@ rem_mv <- function(diffexp=list(), pcriteria="pvalue", foldchangecol="Log2FC",
 		   genenamecol="Symbol", geneidcol=NULL, collaps=FALSE, 
 		   llcol="CI.L", rlcol="CI.R", vcol=NULL, cvar=TRUE, 
 		   metathr=0.01, jobname="MetaVolcano", outputfolder=".", 
-		   draw='HTML', ncores=1) {
+		   draw='HTML', ncores=1, render = F) {
 
 
     if(!draw %in% c('PDF', 'HTML')) {
@@ -199,24 +204,28 @@ rem_mv <- function(diffexp=list(), pcriteria="pvalue", foldchangecol="Log2FC",
     # --- Draw REM MetaVolcano
     gg <- plot_rem(meta_diffexp, jobname, outputfolder, genecol, metathr)
 
-    if(draw == "HTML") {
+    if(render) {
+
+      if(draw == "HTML") {
 
         # --- Writing html device for offline visualization
         saveWidget(as_widget(ggplotly(gg)), 
-            paste0(normalizePath(outputfolder), 
-	           "/RandomEffectModel_MetaVolcano_", 
-	           jobname, ".html"))
-
-   } else if(draw == "PDF") {
-
+                   paste0(normalizePath(outputfolder), 
+                          "/RandomEffectModel_MetaVolcano_", 
+                          jobname, ".html"))
+        
+      } else if(draw == "PDF") {
+        
         # --- Writing PDF visualization
-	pdf(paste0(normalizePath(outputfolder),
-	           "/RandomEffectModel_MetaVolcano_", jobname,
-	           ".pdf"), width = 7, height = 6)
-	     plot(gg)
-	dev.off()
-
-    } 
+        pdf(paste0(normalizePath(outputfolder),
+                   "/RandomEffectModel_MetaVolcano_", jobname,
+                   ".pdf"), width = 7, height = 6)
+        plot(gg)
+        dev.off()
+
+      }
+
+    }
 
     # Set REM result
     icols <- paste(c(genecol, pcriteria, foldchangecol, llcol, rlcol, vcol),