plotCommunitiesStats: Plot general structure & connectivity statistics for each...

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

Plot general structure & connectivity statistics for each community in a filtered GRN

Description

Similarly to the statistics produced by plotGeneralGraphStats, summaries regarding the vertex degrees and the most important vertices per community are generated. Note that the communities need to first be calculated using the calculateCommunitiesStats function

Usage

plotCommunitiesStats(
  GRN,
  outputFolder = NULL,
  basenameOutput = NULL,
  display = "byRank",
  communities = seq_len(10),
  topnGenes = 20,
  topnTFs = 20,
  plotAsPDF = TRUE,
  pdf_width = 12,
  pdf_height = 12,
  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)
display	Character. Default "byRank". One of: "byRank", "byLabel". Specify whether the communities will by displayed based on their rank, where the largest community (with most vertices) would have a rank of 1, or by their label. Note that the label is independent of the rank.
communities	Numeric vector. Default seq_len(10). Depending on what was specified in the display parameter, this parameter would indicate either the rank or the label of the communities to be plotted. i.e. for communities = c(1,4), if display = "byRank" the results for the first and fourth largest communities will be plotted. if display = "byLabel", the results for the communities labeled "1", and "4" will be plotted. If set to NULL, all communities will be plotted
topnGenes	Integer. Default 20. Number of genes to plot, sorted by their rank or label.
topnTFs	Integer. Default 20. Number of TFs to plot, sorted by their rank or label.
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. A single PDF file is produced with the statistics.

See Also

plotGeneralGraphStats

calculateCommunitiesStats

calculateCommunitiesEnrichment

Examples

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

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