Plot diagnostic plots for TF-peak connections for a GRN object

  outputFolder = NULL,
  basenameOutput = NULL,
  plotDetails = FALSE,
  dataType = c("real", "background"),
  nTFMax = NULL,
  plotAsPDF = TRUE,
  pdf_width = 12,
  pdf_height_base = 8,
  pages = NULL,
  forceRerun = FALSE



Object of class GRN


Character or NULL. Default NULL. If set to NULL, the default output folder as specified when initiating the object in initializeGRN will be used. Otherwise, all output from this function will be put into the specified folder. If a folder is provided, while we recommend specifying an absolute path, a relative one also works.


NULL or character. Default NULL. Basename of the output files that are produced. If set to NULL, a default basename is chosen. If a custom basename is specified, all output files will have the chosen basename as file prefix, be careful with not overwriting already existing files (if forceRerun is set to TRUE)


TRUE or FALSE. Default FALSE. Print additional plots that may help for debugging and QC purposes? Note that these plots are currently less documented or not at all.


Character vector. One of, or both of, "real" or "background". For which type, real or background data, to produce the diagnostic plots?


NULL or Integer > 0. Default NULL. Maximum number of TFs to process. Can be used for testing purposes by setting this to a small number i(.e., 10)


TRUE or FALSE. Default TRUE.Should the plots be printed to a PDF file? If set to TRUE, a PDF file is generated, the name of which depends on the value of basenameOutput. If set to FALSE, all plots are printed to the currently active device. Note that most functions print more than one plot, which means you may only see the last plot depending on your active graphics device.


Number>0. Default 12. Width of the PDF, in cm.


Number. Default 8. Base height of the PDF, in cm, per connection type. The total height is automatically determined based on the number of connection types that are found in the object (e.g., expression or TF activity). For example, when two connection types are found, the base height is multiplied by 2.


Integer vector or NULL. Default NULL. Page number(s) to plot. Can be used to plot only specific pages to a PDF or the currently active graphics device.


TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.


An updated GRN object.


# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
#> Downloading GRaNIE example object from
#> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing!
GRN = plotDiagnosticPlots_TFPeaks(GRN, outputFolder = ".", dataType = "real", nTFMax = 2, pages = 1)
#> INFO [2024-04-04 17:39:11] 
#>  Plotting for real data
#> INFO [2024-04-04 17:39:11] Finished successfully. Execution time: 0 secs