Plot the general enrichement results

This function plots the results of the general enrichment analysis for every specified ontology.

plotGeneralEnrichment(
  GRN,
  outputFolder = NULL,
  basenameOutput = NULL,
  ontology = NULL,
  topn_pvalue = 30,
  p = 0.05,
  display_pAdj = FALSE,
  maxWidth_nchar_plot = 50,
  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 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.

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)

ontology

Character. NULL or vector of ontology names. Default NULL. Vector of ontologies to plot. The results must have been previously calculated otherwise an error is thrown.

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.

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 50. Maximum number of characters for a term before it is truncated.

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

pdf_height

Number >0. 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.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
#> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds
#> INFO [2023-08-16 17:29:35] Storing GRN@data$RNA$counts matrix as sparse matrix because fraction of 0s is > 0.1 (0.44)
#> 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 = plotGeneralEnrichment(GRN, plotAsPDF = FALSE, pages = 1)
#> INFO [2023-08-16 17:29:35] Plotting directly
#> INFO [2023-08-16 17:29:35] Found the following ontology results for plotting: GO_BP,GO_MF
#> INFO [2023-08-16 17:29:35] Plotting for the following user-selected ontologies: GO_BP,GO_MF
#> INFO [2023-08-16 17:29:35]  Ontology GO_BP

#> INFO [2023-08-16 17:29:36]  Ontology GO_MF
#> INFO [2023-08-16 17:29:36]  Finished successfully. Execution time: 0.5 secs