@@ -1654,7 +1654,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05

         suffixFile = .getPermutationSuffixStr(permutationCur)

-        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_density"), "_", connectionTypeCur, suffixFile)

+        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_density"), "_", connectionTypeCur, suffixFile, ".pdf")

         if (!file.exists(fileCur) | forceRerun) {

           .plot_density(.asMatrixFromSparse(GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_peak_cor_foreground),

                         .asMatrixFromSparse(GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_peak_cor_background), 

@@ -1664,7 +1664,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05

           futile.logger::flog.info(paste0("  File ", fileCur, " already exists, not overwriting since forceRerun = FALSE"))

         }

-        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_medianClass"), "_", connectionTypeCur, suffixFile)

+        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_medianClass"), "_", connectionTypeCur, suffixFile, ".pdf")

         if (!file.exists(fileCur) | forceRerun) {

           .plot_AR_thresholds(

             median.cor.tfs = .asMatrixFromSparse(GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_cor_median_foreground), 

@@ -1677,7 +1677,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05

           futile.logger::flog.info(paste0("  File ", fileCur, " already exists, not overwriting since forceRerun = FALSE"))

         }

-        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_densityClass"), "_", connectionTypeCur, suffixFile)

+        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_densityClass"), "_", connectionTypeCur, suffixFile, ".pdf")

         if (!file.exists(fileCur) | forceRerun) {

           TF_peak_cor = GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_peak_cor

@@ -3171,7 +3171,7 @@ filterGRNAndConnectGenes <- function(GRN,

         suffixFile = .getPermutationSuffixStr(permutationCur)

         outputFolder = .checkOutputFolder(GRN, outputFolder)

-        outputFile = paste0(outputFolder, .getOutputFileName("plot_peakGene_IHW_diag"), suffixFile)

+        outputFile = paste0(outputFolder, .getOutputFileName("plot_peakGene_IHW_diag"), suffixFile, ".pdf")

         IHW.res = .performIHW(grn.filt$peak_gene.p_raw[indexes], 

                               covariate_val[indexes] %>% unlist() %>% unname(), 

@@ -546,7 +546,7 @@ plotDiagnosticPlots_TFPeaks <- function(GRN,

     }

     # TODO: page selection not implemented here yet

-    fileCur = paste0(outputFolder, .getOutputFileName("plot_TFPeak_fdr_GC"), suffixFile)

+    fileCur = paste0(outputFolder, .getOutputFileName("plot_TFPeak_fdr_GC"), suffixFile, ".pdf")

     if (useGCCorrection & (!file.exists(fileCur) | !plotAsPDF | forceRerun)) {

         if (!plotAsPDF) fileCur = NULL

@@ -3365,7 +3365,7 @@ visualizeGRN <- function(GRN, outputFolder = NULL,  basenameOutput = NULL, plotA

     if (plotAsPDF) {

         futile.logger::flog.info(paste0("Plotting GRN network to ", outputFolder, dplyr::if_else(is.null(basenameOutput), .getOutputFileName("plot_network"), basenameOutput),".pdf"))

-        grDevices::pdf(file = paste0(outputFolder,"/", ifelse(is.null(basenameOutput), .getOutputFileName("plot_network"), basenameOutput),".pdf"),width = pdf_width, height = pdf_height )

+        grDevices::pdf(file = paste0(outputFolder,"/", ifelse(is.null(basenameOutput), .getOutputFileName("plot_network"), basenameOutput),".pdf"), width = pdf_width, height = pdf_height )

     } else {

         futile.logger::flog.info(paste0("Plotting GRN network"))

     }