@@ -1,6 +1,6 @@

 Package: GRaNIE

 Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

-Version: 0.99.2

+Version: 0.99.3

 Encoding: UTF-8

 Authors@R: c(person("Christian", "Arnold", email =

         "chrarnold@web.de", role = c("cre","aut")),

@@ -1731,7 +1731,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' GRN = addConnections_TF_peak(GRN, outputFolder = ".", forceRerun = FALSE)

+#' GRN = addConnections_TF_peak(GRN, plotDiagnosticPlots = FALSE, forceRerun = FALSE)

 #' @export

 addConnections_TF_peak <- function (GRN, plotDiagnosticPlots = TRUE, plotDetails = FALSE, outputFolder = NULL, 

                                     corMethod = "pearson", 

@@ -2277,8 +2277,7 @@ addConnections_TF_peak <- function (GRN, plotDiagnosticPlots = TRUE, plotDetails

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' types =  list(c("protein_coding"))

-#' GRN = addConnections_peak_gene(GRN, promoterRange=10000, outputFolder=".", plotGeneTypes=types)

+#' GRN = addConnections_peak_gene(GRN, promoterRange=10000, plotDiagnosticPlots = FALSE)

 addConnections_peak_gene <- function(GRN, overlapTypeGene = "TSS", corMethod = "pearson",

                                      promoterRange = 250000, TADs = NULL,

                                      nCores = 4, 

@@ -3937,7 +3936,7 @@ loadExampleObject <- function(forceDownload = FALSE, fileURL = "https://www.embl

   if (!length(rid)) {

     rid <- names(BiocFileCache::bfcadd(bfc, "GRaNIE_object_example", fileURL))

   }

-  if (isFALSE(BiocFileCache::bfcneedsupdate(bfc, rid)) | forceDownload) {

+  if (!isFALSE(BiocFileCache::bfcneedsupdate(bfc, rid)) | forceDownload) {

     messageStr = paste0("Downloading GRaNIE example object from ", fileURL)

     message(messageStr)

     filePath = BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)

@@ -16,8 +16,8 @@

 #' @return The same \code{\linkS4class{GRN}} object, without modifications. In addition, for each specified \code{type}, a PDF file is produced with a PCA. We refer to the Vignettes for details and further explanations.

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

-#' GRN = loadExampleObject()

-#' GRN = plotPCA_all(GRN, topn = 500, outputFolder = ".", type = "rna", plotAsPDF=FALSE)

+#' # GRN = loadExampleObject()

+#' # GRN = plotPCA_all(GRN, topn = 500, type = "rna", plotAsPDF = FALSE)

 #' @export

 plotPCA_all <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 

                         type = c("rna", "peaks"), topn = c(500,1000,5000), 

@@ -809,7 +809,7 @@ plotDiagnosticPlots_TFPeaks <- function(GRN,

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' # GRN = loadExampleObject()

 #' # types = list(c("protein_coding"))

-#' # GRN = plotDiagnosticPlots_peakGene(GRN, outputFolder=".", gene.types=types, plotAsPDF=FALSE)

+#' # GRN = plotDiagnosticPlots_peakGene(GRN, gene.types=types, plotAsPDF = FALSE)

 #' @export

 # TODO: implement forceRerun correctly

 plotDiagnosticPlots_peakGene <- function(GRN, 

@@ -1599,7 +1599,7 @@ plotDiagnosticPlots_peakGene <- function(GRN,

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' GRN = plot_stats_connectionSummary(GRN, outputFolder = ".", forceRerun = FALSE, plotAsPDF=FALSE)

+#' GRN = plot_stats_connectionSummary(GRN, forceRerun = FALSE, plotAsPDF = FALSE)

 #' @export

 #' @importFrom circlize colorRamp2

 plot_stats_connectionSummary <- function(GRN, type = "heatmap", 

@@ -1931,7 +1931,7 @@ plot_stats_connectionSummary <- function(GRN, type = "heatmap",

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' GRN = plotGeneralGraphStats(GRN, outputFolder = ".", plotAsPDF=FALSE)

+#' GRN = plotGeneralGraphStats(GRN, plotAsPDF = FALSE)

 #' @export

 plotGeneralGraphStats <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 

                                   plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12, 

@@ -2097,7 +2097,7 @@ plotGeneralGraphStats <- function(GRN, outputFolder = NULL, basenameOutput = NUL

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' GRN = plotGeneralEnrichment(GRN, outputFolder = ".", plotAsPDF=FALSE)

+#' GRN = plotGeneralEnrichment(GRN, plotAsPDF = FALSE)

 #' @export

 plotGeneralEnrichment <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 

                                   ontology = NULL, topn_pvalue = 30, p = 0.05, 

@@ -2276,7 +2276,7 @@ plotGeneralEnrichment <- function(GRN, outputFolder = NULL, basenameOutput = NUL

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' GRN = plotCommunitiesStats(GRN, outputFolder = ".", plotAsPDF=FALSE)

+#' GRN = plotCommunitiesStats(GRN, plotAsPDF = FALSE)

 #' @export

 plotCommunitiesStats <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 

                                  display = "byRank", communities = seq_len(10), 

@@ -2446,7 +2446,7 @@ plotCommunitiesStats <- function(GRN, outputFolder = NULL, basenameOutput = NULL

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' GRN = plotCommunitiesEnrichment(GRN, outputFolder = ".", plotAsPDF=FALSE)

+#' GRN = plotCommunitiesEnrichment(GRN, plotAsPDF = FALSE)

 #' @export

 #' @import ggplot2

 #' @importFrom grid gpar

@@ -2760,7 +2760,7 @@ plotCommunitiesEnrichment <- function(GRN, outputFolder = NULL, basenameOutput =

 #' @examples 

 #' # See the Workflow vignette on the GRaNIE website for examples

 #' GRN = loadExampleObject()

-#' GRN = plotTFEnrichment(GRN, n = 5, outputFolder = ".", plotAsPDF=FALSE)

+#' GRN = plotTFEnrichment(GRN, n = 5, plotAsPDF = FALSE)

 #' @export

 #' @importFrom grid gpar

 plotTFEnrichment <- function(GRN, rankType = "degree", n = NULL, TF.names = NULL,

Binary files a/R/sysdata.rda and b/R/sysdata.rda differ