plotDiagnosticPlots_TFPeaks: Plot diagnostic plots for TF-peak connections for a 'GRN'...

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

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

Description

Due to the number of plots that this functions produces, we currently provide only the option to plot as PDF. This may change in the future.

Usage

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

Arguments

GRN	Object of class GRN
outputFolder	Character or NULL. Default NULL. If set to NULL, the default output folder as specified when initiating the object in link{initializeGRN} will be used. Otherwise, all output from this function will be put into the specified folder. We recommend specifying an absolute path.
basenameOutput	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)
plotDetails	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.
dataType	Character vector. One of, or both of, "real" or "permuted". For which data type, real or permuted data, to produce the diagnostic plots?
nTFMax	NULL or Integer. Default NULL. Maximum number of TFs to process. Can be used for testing purposes by setting this to a small number i(.e., 10)
plotAsPDF	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.
pdf_width	Number. Default 12. Width of the PDF, in cm.
pdf_height_base	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.
pages	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.
forceRerun	TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.

Value

The same GRN object, with added data from this function.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
GRN = plotDiagnosticPlots_TFPeaks(GRN, outputFolder = ".", dataType = "real", nTFMax = 2)

chrarnold/GRaNIE documentation built on April 28, 2022, 2:18 a.m.