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Attempts to aim to decrease the build time, corrected BiocFileCache code assuming the expiration date is solved, rebuild sysdata.rda to make it smaller

Christian Arnold authored on 21/03/2022 23:24:45
Showing4 changed files

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@@ -1,6 +1,6 @@
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 Package: GRaNIE
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 Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
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-Version: 0.99.2
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+Version: 0.99.3
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 Encoding: UTF-8
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 Authors@R: c(person("Christian", "Arnold", email =
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         "chrarnold@web.de", role = c("cre","aut")),
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@@ -1731,7 +1731,7 @@ AR_classification_wrapper<- function (GRN, significanceThreshold_Wilcoxon = 0.05
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' GRN = addConnections_TF_peak(GRN, outputFolder = ".", forceRerun = FALSE)
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+#' GRN = addConnections_TF_peak(GRN, plotDiagnosticPlots = FALSE, forceRerun = FALSE)
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 #' @export
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 addConnections_TF_peak <- function (GRN, plotDiagnosticPlots = TRUE, plotDetails = FALSE, outputFolder = NULL, 
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                                     corMethod = "pearson", 
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@@ -2277,8 +2277,7 @@ addConnections_TF_peak <- function (GRN, plotDiagnosticPlots = TRUE, plotDetails
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' types =  list(c("protein_coding"))
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-#' GRN = addConnections_peak_gene(GRN, promoterRange=10000, outputFolder=".", plotGeneTypes=types)
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+#' GRN = addConnections_peak_gene(GRN, promoterRange=10000, plotDiagnosticPlots = FALSE)
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 addConnections_peak_gene <- function(GRN, overlapTypeGene = "TSS", corMethod = "pearson",
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                                      promoterRange = 250000, TADs = NULL,
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                                      nCores = 4, 
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@@ -3937,7 +3936,7 @@ loadExampleObject <- function(forceDownload = FALSE, fileURL = "https://www.embl
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   if (!length(rid)) {
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     rid <- names(BiocFileCache::bfcadd(bfc, "GRaNIE_object_example", fileURL))
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   }
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-  if (isFALSE(BiocFileCache::bfcneedsupdate(bfc, rid)) | forceDownload) {
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+  if (!isFALSE(BiocFileCache::bfcneedsupdate(bfc, rid)) | forceDownload) {
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     messageStr = paste0("Downloading GRaNIE example object from ", fileURL)
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     message(messageStr)
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     filePath = BiocFileCache::bfcdownload(bfc, rid, ask = FALSE)
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@@ -16,8 +16,8 @@
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 #' @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.
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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-#' GRN = loadExampleObject()
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-#' GRN = plotPCA_all(GRN, topn = 500, outputFolder = ".", type = "rna", plotAsPDF=FALSE)
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+#' # GRN = loadExampleObject()
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+#' # GRN = plotPCA_all(GRN, topn = 500, type = "rna", plotAsPDF = FALSE)
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 #' @export
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 plotPCA_all <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 
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                         type = c("rna", "peaks"), topn = c(500,1000,5000), 
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@@ -809,7 +809,7 @@ plotDiagnosticPlots_TFPeaks <- function(GRN,
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' # GRN = loadExampleObject()
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 #' # types = list(c("protein_coding"))
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-#' # GRN = plotDiagnosticPlots_peakGene(GRN, outputFolder=".", gene.types=types, plotAsPDF=FALSE)
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+#' # GRN = plotDiagnosticPlots_peakGene(GRN, gene.types=types, plotAsPDF = FALSE)
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 #' @export
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 # TODO: implement forceRerun correctly
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 plotDiagnosticPlots_peakGene <- function(GRN, 
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@@ -1599,7 +1599,7 @@ plotDiagnosticPlots_peakGene <- function(GRN,
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' GRN = plot_stats_connectionSummary(GRN, outputFolder = ".", forceRerun = FALSE, plotAsPDF=FALSE)
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+#' GRN = plot_stats_connectionSummary(GRN, forceRerun = FALSE, plotAsPDF = FALSE)
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 #' @export
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 #' @importFrom circlize colorRamp2
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 plot_stats_connectionSummary <- function(GRN, type = "heatmap", 
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@@ -1931,7 +1931,7 @@ plot_stats_connectionSummary <- function(GRN, type = "heatmap",
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' GRN = plotGeneralGraphStats(GRN, outputFolder = ".", plotAsPDF=FALSE)
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+#' GRN = plotGeneralGraphStats(GRN, plotAsPDF = FALSE)
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 #' @export
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 plotGeneralGraphStats <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 
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                                   plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12, 
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@@ -2097,7 +2097,7 @@ plotGeneralGraphStats <- function(GRN, outputFolder = NULL, basenameOutput = NUL
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' GRN = plotGeneralEnrichment(GRN, outputFolder = ".", plotAsPDF=FALSE)
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+#' GRN = plotGeneralEnrichment(GRN, plotAsPDF = FALSE)
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 #' @export
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 plotGeneralEnrichment <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 
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                                   ontology = NULL, topn_pvalue = 30, p = 0.05, 
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@@ -2276,7 +2276,7 @@ plotGeneralEnrichment <- function(GRN, outputFolder = NULL, basenameOutput = NUL
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' GRN = plotCommunitiesStats(GRN, outputFolder = ".", plotAsPDF=FALSE)
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+#' GRN = plotCommunitiesStats(GRN, plotAsPDF = FALSE)
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 #' @export
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 plotCommunitiesStats <- function(GRN, outputFolder = NULL, basenameOutput = NULL, 
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                                  display = "byRank", communities = seq_len(10), 
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@@ -2446,7 +2446,7 @@ plotCommunitiesStats <- function(GRN, outputFolder = NULL, basenameOutput = NULL
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' GRN = plotCommunitiesEnrichment(GRN, outputFolder = ".", plotAsPDF=FALSE)
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+#' GRN = plotCommunitiesEnrichment(GRN, plotAsPDF = FALSE)
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 #' @export
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 #' @import ggplot2
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 #' @importFrom grid gpar
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@@ -2760,7 +2760,7 @@ plotCommunitiesEnrichment <- function(GRN, outputFolder = NULL, basenameOutput =
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 #' @examples 
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 #' # See the Workflow vignette on the GRaNIE website for examples
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 #' GRN = loadExampleObject()
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-#' GRN = plotTFEnrichment(GRN, n = 5, outputFolder = ".", plotAsPDF=FALSE)
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+#' GRN = plotTFEnrichment(GRN, n = 5, plotAsPDF = FALSE)
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 #' @export
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 #' @importFrom grid gpar
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 plotTFEnrichment <- function(GRN, rankType = "degree", n = NULL, TF.names = NULL,
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Binary files a/R/sysdata.rda and b/R/sysdata.rda differ