Browse code

Added missing pdf suffix for AR classification

Christian Arnold authored on 25/04/2022 16:49:49
Showing2 changed files

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@@ -1654,7 +1654,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05
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         suffixFile = .getPermutationSuffixStr(permutationCur)
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-        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_density"), "_", connectionTypeCur, suffixFile)
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+        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_density"), "_", connectionTypeCur, suffixFile, ".pdf")
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         if (!file.exists(fileCur) | forceRerun) {
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           .plot_density(.asMatrixFromSparse(GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_peak_cor_foreground),
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                         .asMatrixFromSparse(GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_peak_cor_background), 
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@@ -1664,7 +1664,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05
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           futile.logger::flog.info(paste0("  File ", fileCur, " already exists, not overwriting since forceRerun = FALSE"))
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         }
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-        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_medianClass"), "_", connectionTypeCur, suffixFile)
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+        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_medianClass"), "_", connectionTypeCur, suffixFile, ".pdf")
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         if (!file.exists(fileCur) | forceRerun) {
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           .plot_AR_thresholds(
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             median.cor.tfs = .asMatrixFromSparse(GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_cor_median_foreground), 
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@@ -1677,7 +1677,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05
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           futile.logger::flog.info(paste0("  File ", fileCur, " already exists, not overwriting since forceRerun = FALSE"))
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         }
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-        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_densityClass"), "_", connectionTypeCur, suffixFile)
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+        fileCur = paste0(outputFolder, .getOutputFileName("plot_class_densityClass"), "_", connectionTypeCur, suffixFile, ".pdf")
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         if (!file.exists(fileCur) | forceRerun) {
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           TF_peak_cor = GRN@data$TFs$classification[[permIndex]] [[connectionTypeCur]]$TF_peak_cor
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@@ -3171,7 +3171,7 @@ filterGRNAndConnectGenes <- function(GRN,
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         suffixFile = .getPermutationSuffixStr(permutationCur)
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         outputFolder = .checkOutputFolder(GRN, outputFolder)
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-        outputFile = paste0(outputFolder, .getOutputFileName("plot_peakGene_IHW_diag"), suffixFile)
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+        outputFile = paste0(outputFolder, .getOutputFileName("plot_peakGene_IHW_diag"), suffixFile, ".pdf")
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         IHW.res = .performIHW(grn.filt$peak_gene.p_raw[indexes], 
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                               covariate_val[indexes] %>% unlist() %>% unname(), 
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@@ -546,7 +546,7 @@ plotDiagnosticPlots_TFPeaks <- function(GRN,
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     }
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     # TODO: page selection not implemented here yet
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-    fileCur = paste0(outputFolder, .getOutputFileName("plot_TFPeak_fdr_GC"), suffixFile)
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+    fileCur = paste0(outputFolder, .getOutputFileName("plot_TFPeak_fdr_GC"), suffixFile, ".pdf")
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     if (useGCCorrection & (!file.exists(fileCur) | !plotAsPDF | forceRerun)) {
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         if (!plotAsPDF) fileCur = NULL
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@@ -3365,7 +3365,7 @@ visualizeGRN <- function(GRN, outputFolder = NULL,  basenameOutput = NULL, plotA
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     if (plotAsPDF) {
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         futile.logger::flog.info(paste0("Plotting GRN network to ", outputFolder, dplyr::if_else(is.null(basenameOutput), .getOutputFileName("plot_network"), basenameOutput),".pdf"))
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-        grDevices::pdf(file = paste0(outputFolder,"/", ifelse(is.null(basenameOutput), .getOutputFileName("plot_network"), basenameOutput),".pdf"),width = pdf_width, height = pdf_height )
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+        grDevices::pdf(file = paste0(outputFolder,"/", ifelse(is.null(basenameOutput), .getOutputFileName("plot_network"), basenameOutput),".pdf"), width = pdf_width, height = pdf_height )
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     } else {
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         futile.logger::flog.info(paste0("Plotting GRN network"))
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     }