plotTFEnrichment: Plot TF-based GO enrichment results

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

Plot TF-based GO enrichment results

Description

This function plots the enrichment results. The result consist of a dot plot per specified TF, as well as two comparative heatmaps. The first heatmap displays the p value for each GO term across the TFs. Terms that The second heatmap is a subset of the first, where select terms are kept or filtered out for better visibility and display.

Usage

plotTFEnrichment(
  GRN,
  rankType = "degree",
  n = NULL,
  TF.names = NULL,
  topn_pvalue = 30,
  p = 0.05,
  nSignificant = 2,
  nID = 10,
  display_pAdj = FALSE,
  maxWidth_nchar_plot = 100,
  outputFolder = NULL,
  basenameOutput = NULL,
  plotAsPDF = TRUE,
  pdf_width = 12,
  pdf_height = 12,
  pages = NULL,
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
rankType	Character. One of: "degree", "EV", "custom". This parameter will determine the criterion to be used to identify the "top" nodes. If set to "degree", the function will select top nodes based on the number of connections they have, i.e. based on their degree-centrality. If set to "EV" it will select the top nodes based on their eigenvector-centrality score in the network.
n	NULL or numeric. Default NULL. If set to NULL, all previously calculated TF enrichments will be plotted. If set to a value between (0,1), it is treated as a percentage of top nodes. If the value is passed as an integer it will be treated as the number of top nodes. This parameter is not relevant if rankType = "custom".
TF.names	NULL or character vector. Default NULL. For rankType="custom" the names of the TFs to plot. Ignored otherwise.
topn_pvalue	Numeric. Default 30. Maximum number of ontology terms that meet the p-value significance threshold to display in the enrichment dot plot
p	Numeric. Default 0.05. p-value threshold to determine significance.
nSignificant	Numeric. Default 3. Threshold to filter out an ontology term with less than nSignificant overlapping genes.
nID	Numeric. Default 10. For the reduced heatmap, number of top terms to select per community.
display_pAdj	TRUE or FALSE. Default FALSE. Is the p-value being displayed in the plots the adjusted p-value? This parameter is relevant for KEGG, Disease Ontology, and Reactome enrichments, and does not affect GO enrichments.
maxWidth_nchar_plot	Integer (>=10). Default 100. Maximum number of characters for a term before it is truncated.
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. A single PDF file is produced with the results.

See Also

calculateTFEnrichment

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
GRN = plotTFEnrichment(GRN, n = 5, plotAsPDF = FALSE)

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