plot_stats_connectionSummary: Plot various network connectivity summaries for a 'GRN'...

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

Plot various network connectivity summaries for a GRN object

Description

Plot various network connectivity summaries for a GRN object

Usage

plot_stats_connectionSummary(
  GRN,
  type = "heatmap",
  outputFolder = NULL,
  basenameOutput = NULL,
  plotAsPDF = TRUE,
  pdf_width = 12,
  pdf_height = 12,
  pages = NULL,
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
type	Character. Either "heatmap" or "boxplot". Default "heatmap". Which plot type to produce?
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)
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	Number. Default 12. Height of the PDF, in cm.
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, without modifications. In addition, for the specified type, a PDF file (default filename is GRN.connectionSummary_{type}.pdf) is produced with a connection summary.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
GRN = plot_stats_connectionSummary(GRN, forceRerun = FALSE, plotAsPDF = FALSE)

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