@@ -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: 1.1.13

+Version: 1.1.14

 Encoding: UTF-8

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

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

@@ -3966,6 +3966,7 @@ generateStatsSummary <- function(GRN,

                 futile.logger::flog.debug(paste0("    TF_peak.connectionType = ", TF_peak.connectionTypeCur))

+                futile.logger::flog.threshold(futile.logger::WARN)

                 GRN = filterGRNAndConnectGenes(GRN, 

                                                TF_peak.fdr.threshold = TF_peak.fdr_cur, 

                                                TF_peak.connectionTypes = TF_peak.connectionTypeCur, 

@@ -3976,7 +3977,10 @@ generateStatsSummary <- function(GRN,

                                                allowMissingTFs = allowMissingTFsCur,

                                                peak_gene.r_range = peak_gene.r_range,

                                                filterTFs = NULL, filterGenes = NULL, filterPeaks = NULL,

-                                               silent = TRUE)

+                                               silent = FALSE)

+                

+                futile.logger::flog.threshold(futile.logger::INFO)

+                

                 results.l = .addStats(GRN@stats$connections, GRN@connections$all.filtered[[permIndex]], 

                                       perm = permutationCur, 

@@ -4217,6 +4221,11 @@ loadExampleObject <- function(forceDownload = FALSE, fileURL = "https://www.embl

   GRN = .makeObjectCompatible(GRN)

+  # TODO remove once done already in the object

+  GRN = add_TF_gene_correlation(GRN)

+  

+  # GRN = add_featureVariation(GRN, formula = "auto", metadata = "mt_frac")

+  

   GRN

 }

@@ -2166,6 +2166,7 @@ plotGeneralGraphStats <- function(GRN, outputFolder = NULL, basenameOutput = NUL

 #' @return The same \code{\linkS4class{GRN}} object, without modifications.

 #' @seealso \code{\link{plotCommunitiesEnrichment}}

 #' @seealso \code{\link{plotTFEnrichment}}

+#' @seealso \code{\link{calculateGeneralEnrichment}}

 #' @examples 

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

 #' GRN = loadExampleObject()

@@ -2194,6 +2195,7 @@ plotGeneralEnrichment <- function(GRN, outputFolder = NULL, basenameOutput = NUL

   checkmate::assertNumeric(p, lower = 0, upper = 1)

   checkmate::assertIntegerish(topn_pvalue, lower = 1)

   checkmate::assertFlag(display_pAdj)

+  checkmate::assertIntegerish(maxWidth_nchar_plot, lower = 10)

   checkmate::assertFlag(plotAsPDF)

   checkmate::assertNumeric(pdf_width, lower = 5, upper = 99)

   checkmate::assertNumeric(pdf_height, lower = 5, upper = 99)

@@ -2546,6 +2548,7 @@ plotCommunitiesStats <- function(GRN, outputFolder = NULL, basenameOutput = NULL

 #' @return  The same \code{\linkS4class{GRN}} object, without modifications.

 #' @seealso \code{\link{plotGeneralEnrichment}}

 #' @seealso \code{\link{plotTFEnrichment}}

+#' @seealso \code{\link{calculateCommunitiesEnrichment}}

 #' @examples 

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

 #' GRN = loadExampleObject()

@@ -2574,7 +2577,7 @@ plotCommunitiesEnrichment <- function(GRN, outputFolder = NULL, basenameOutput =

   checkmate::assertNumeric(nID, lower = 1)

   checkmate::assertFlag(display_pAdj)

   checkmate::assertFlag(plotAsPDF)

-  checkmate::assertIntegerish(maxWidth_nchar_plot, lower = 10, upper = 500)

+  checkmate::assertIntegerish(maxWidth_nchar_plot, lower = 10)

   checkmate::assertNumeric(pdf_width, lower = 5, upper = 99)

   checkmate::assertNumeric(pdf_height, lower = 5, upper = 99)

   checkmate::assert(checkmate::checkNull(pages), checkmate::checkIntegerish(pages, lower = 1))

@@ -2891,6 +2894,7 @@ plotCommunitiesEnrichment <- function(GRN, outputFolder = NULL, basenameOutput =

 #' @return The same \code{\linkS4class{GRN}} object, without modifications.

 #' @seealso \code{\link{plotGeneralEnrichment}}

 #' @seealso \code{\link{plotCommunitiesEnrichment}}

+#' @seealso \code{\link{calculateTFEnrichment}}

 #' @examples 

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

 #' GRN = loadExampleObject()

@@ -2924,6 +2928,7 @@ plotTFEnrichment <- function(GRN, rankType = "degree", n = NULL, TF.names = NULL

   checkmate::assertNumeric(pdf_height, lower = 5, upper = 99)

   checkmate::assert(checkmate::checkNull(pages), checkmate::checkIntegerish(pages, lower = 1))

   checkmate::assertFlag(display_pAdj)

+  checkmate::assertIntegerish(maxWidth_nchar_plot, lower = 10)

   checkmate::assert(checkmate::checkNull(outputFolder), checkmate::checkCharacter(outputFolder, min.chars = 1))

   checkmate::assert(checkmate::checkNull(basenameOutput), checkmate::checkCharacter(basenameOutput, len = 1, min.chars = 1, any.missing = FALSE))

   checkmate::assertFlag(forceRerun)

@@ -74,4 +74,6 @@ GRN = plotCommunitiesEnrichment(GRN, plotAsPDF = FALSE, pages = 1)

 \code{\link{plotGeneralEnrichment}}

 \code{\link{plotTFEnrichment}}

+

+\code{\link{calculateCommunitiesEnrichment}}

 }

@@ -62,4 +62,6 @@ GRN = plotGeneralEnrichment(GRN, plotAsPDF = FALSE, pages = 1)

 \code{\link{plotCommunitiesEnrichment}}

 \code{\link{plotTFEnrichment}}

+

+\code{\link{calculateGeneralEnrichment}}

 }

@@ -77,4 +77,6 @@ GRN = plotTFEnrichment(GRN, n = 5, plotAsPDF = FALSE, pages = 1)

 \code{\link{plotGeneralEnrichment}}

 \code{\link{plotCommunitiesEnrichment}}

+

+\code{\link{calculateTFEnrichment}}

 }

deleted file mode 100644

@@ -1,52 +0,0 @@

-test_that("multiplication works", {

-  expect_equal(2 * 2, 4)

-})

-

-test_that("addConnections_TF_peak", {

-  options(timeout = 500)

-  GRN = loadExampleObject(forceDownload = TRUE)

-  

-  GRN = addConnections_TF_peak(GRN, connectionTypes = c("expression"), outputFolder = ".", forceRerun = TRUE)

-  expect_s4_class(GRN, "GRN")

-  

-  expect_error(addConnections_TF_peak(GRN, connectionTypes = c("bla"), outputFolder = ".", forceRerun = TRUE), 

-               regexp = "Assertion on")

-  

-  expect_error(addConnections_TF_peak(GRN, connectionTypes = c("expression", "TF_activity"), outputFolder = ".", forceRerun = TRUE))

-  

-  expect_error(addConnections_TF_peak(GRN, connectionTypes = c("expression", "TF_activity"), outputFolder = ".", forceRerun = TRUE, removeNegativeCorrelation = c(FALSE)), 

-               regexp = "Assertion on")

-  

-  # Make sure TF activity is added now

-  # TODO: Add TF activity here

-  # GRN = addConnections_TF_peak(GRN, connectionTypes = c("expression", "TF_activity"), removeNegativeCorrelation = c(FALSE, TRUE), forceRerun = TRUE)

-  # expect_s4_class(GRN, "GRN")

-  # 

-  # GRN = addConnections_TF_peak(GRN, connectionTypes = c("expression", "TF_activity"), removeNegativeCorrelation = c(TRUE, FALSE), forceRerun = TRUE)

-  # expect_s4_class(GRN, "GRN")

-  # 

-  # GRN = addConnections_TF_peak(GRN, connectionTypes = c("TF_activity"), removeNegativeCorrelation = c(TRUE), forceRerun = TRUE)

-  # expect_s4_class(GRN, "GRN")

-  

-

-})

-

-test_that("AR wrapper", {

-    

-    # We need to increase the timeout, as sometimes, loading this from the internet (here: from our Zaugg download folder) is slow

-    options(timeout = 1000)

-    GRN = loadExampleObject()

-

-    # When we expect an error, we should always try to capture the error by something that is supposed to be captured by the code with a specific error message

-    expect_error(AR_classification_wrapper(GRN, significanceThreshold_Wilcoxon = 1.5, outputFolder = "."),  regexp = "Assertion on")

-    

-    # Run with TF activity and expression

-    GRN = AR_classification_wrapper(GRN, significanceThreshold_Wilcoxon = 0.05,

-                                            plot_minNoTFBS_heatmap = 100, plotDiagnosticPlots = TRUE,

-                                            outputFolder = ".", 

-                                            deleteIntermediateData = TRUE, forceRerun = TRUE)

-    

-    # What happens if TF activity is defined but addConnections_TF_peak with only expression?

-    

-    

-})

@@ -88,7 +88,7 @@ opts_chunk$set(

   cache = FALSE,

   message = FALSE,

   fig.align="center",

-  dpi=300,

+  dpi=200,

   fig.height=8,

   results='hold')

 ```