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Get a Reactome Pathway Overview

Source: R/reactome_content.R
rba_reactome_exporter_overview.Rd

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

Usage

rba_reactome_exporter_overview(
  species,
  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,
  ...
)

Arguments

species

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.

output_format

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

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.

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)

diagram_profile

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

token

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

resource

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

exp_column

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

coverage

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.

Value

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

Corresponding API Resources

"GET https://reactome.org/ContentService/exporter/fireworks/{species}.{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

See also

rba_reactome_analysis

Other "Reactome Content Service - Format Exporter": rba_reactome_exporter_diagram(), rba_reactome_exporter_event(), rba_reactome_exporter_reaction()

Examples

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)
}