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This function will Save a Pathway Overview of the supplied specie as an image file.


  output_format = "png",
  save_to = NULL,
  image_quality = 5,
  flag_element = NULL,
  flg_interactors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  diagram_profile = "Copper",
  token = NULL,
  resource = "TOTAL",
  exp_column = NULL,
  coverage = FALSE,



Numeric or Character: NCBI Taxonomy identifier (Human Taxonomy ID is 9606.) or species name (e.g. "Homo sapiens"). See rba_reactome_species or Reactome Data Schema: Entries: Species.


Images format, Can be one of: png (default), jpeg, svg or gif.


NULL or Character:

  • NULL: Save the file to an automatically-generated path.

  • Character string: A valid file path to save the file to.


Numeric: A number ranging from 1 to 10. 1 is the lowest quality and 10 is the highest (default = 5).


Gene name, protein ID, chemical ID or Reactome ID of a diagram's element to be flagged.


Logical: Should the interactor be considered when flagging a diagram element? (default = TRUE)


CSV line for highlighting element(s) selection in the diagram.


Logical: Should the pathway name be displayed below the image? (default = TRUE)


Numeric: A number ranging from 0 to 20 to set as the image's margin. (default = 15)


Color profile of diagrams, should be one of "Copper" (default), "Copper Plus", "Barium Lithium" or "calcium salts".


The analysis Token for which the results will be overlaid on top of the given pathways overview. see: rba_reactome_analysis.


The analysis resource for which the results will be overlaid on top of the given pathways overview.


numeric: (only if token is supplied) Specify the expression column for the overlay.


Logical: Should the analysis coverage values be overlaid? (default = FALSE)


rbioapi option(s). See rba_options's arguments manual for more information on available options.


NULL, Based to the inputs, an image file will be saved to disk.

Corresponding API Resources



  • Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028,

  • Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

  • Reactome Content Services API Documentation

  • Citations note on Reactome website

See also


if (FALSE) {
rba_reactome_exporter_overview(species = 9606,
    output_format = "svg",
    save_to = "human_pathways.svg")
if (FALSE) {
rba_reactome_exporter_overview(species = 9606,
    token = 123456789)