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This function will Save a Reactome event of class "ReactionLikeEvent" as an image file.

Usage

rba_reactome_exporter_reaction(
  event_id,
  save_to = NULL,
  output_format = "png",
  resource = "TOTAL",
  diagram_profile = "Modern",
  analysis_profile = "Standard",
  token = NULL,
  exp_column = NULL,
  image_quality = 5,
  flag_element = NULL,
  flg_interactors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  ...
)

Arguments

event_id

Reactome Reaction-like event's identifier.

save_to

NULL or Character:

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

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

output_format

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

resource

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

diagram_profile

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

analysis_profile

Color profile of analysis, should be one of: "Standard" (default), "Strosobar" or "Copper Plus".

token

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

exp_column

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

image_quality

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

flag_element

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

flg_interactors

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

sel

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

title

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

margin

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

...

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

Value

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

Details

Note that this function will save Reaction-like event separately and out of it's parent pathway context. To overlay a Reaction on it's parent pathway, use rba_reactome_exporter_diagram.

Corresponding API Resources

"GET https://reactome.org/ContentService//exporter/reaction/ identifier.ext"

References

  • 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, https://doi.org/10.1093/nar/gkab1028

  • 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

Examples

if (FALSE) {
rba_reactome_exporter_diagram(event_id = "R-HSA-6787403",
    create_document = FALSE)
}
if (FALSE) {
rba_reactome_exporter_diagram(event_id = "R-HSA-6787403",
     output_format = "svg",
     save_to = "reactome_reacion_image.svg")
}