Get a Reactome Event Diagram
This function could be called in two scenarios:
With create_document = FALSE: To retrieve an image of that event's Diagram.
With create_document = TRUE: To retrieve a PDF document with the event's diagram image and additional information.
see "Details section" for more information
rba_reactome_exporter_diagram( event_id, save_to = NA, create_document = FALSE, resource = "TOTAL", diagram_profile = "Modern", analysis_profile = "Standard", token = NA, exp_column = NA, document_level = 1, output_format = "png", image_quality = 5, flag_element = NA, flg_interactors = TRUE, sel = NA, title = TRUE, margin = 15, ehld = FALSE, ... )
event_id |
Reactome event's identifier. |
save_to |
NA or Character:
|
create_document |
logical: Create PDF document instead of image? ( default = FALSE) |
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 either "Modern" (default) or "Standard". |
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:
|
exp_column |
numeric: (only if token is provided) Specify the expression column for the overlay. |
document_level |
numeric: (Only if "create_document" is TRUE) if 0 (default) the event's children will not be included in the PDF document. Set this to 1 to include event's children. |
output_format |
(Only if "create_document" is FALSE) Image format of the saved diagram. Can be one of: png (default), jpeg, svg or gif. |
image_quality |
Numeric: (Only if "create_document" is FALSE), a number ranging from 1 to 10. 1 is the lowest quality and 10 is the highest (default = 5). |
flag_element |
(Only if "create_document" is FALSE) gene name, protein ID, chemical ID or Reactome ID of a diagram's element to be flagged. |
flg_interactors |
Logical: (Only if "create_document" is FALSE) Should the interactor be considered when flagging a diagram element? (default = TRUE) |
sel |
(Only if "create_document" is FALSE) CSV line for highlighting element(s) selection in the diagram. |
title |
Logical: (Only if "create_document" is FALSE) Should the pathway name be displayed below the image? (default = TRUE) |
margin |
Numeric: (Only if "create_document" is FALSE) A number ranging from 0 to 20 to set as the image's margin. (default = 15) |
ehld |
logical: (Only if "create_document" is FALSE) Should "Enhanced High Level Diagram" be considered? |
... |
rbioapi option(s). Refer to |
If the function is called with create_document = FALSE:
The result will be an image with the format provided in "output_format"
argument. If the provided event ID refers to a pathway, the image's
content will be the that pathways diagram. If the provided event ID refers
to a sub-pathway or reaction event, the parent pathway's diagram will be
exported, with that reaction or sub-pathway's events highlighted.
Note that to export an image of reaction-like event separately, you
should use rba_reactome_exporter_reaction.
If the function is called with create_document = TRUE:
A PDF document will contain an image of the event's diagram and the
following information of that events: Summation, Literature references,
Edit history type, location, compartments and diseases.
note that if you call the function with "document level = 1", information
of your provided event's children will also be included.
NULL, Based to the inputs, an image or PDF file will be saved to disk.
"GET https://reactome.org/ContentService/exporter/diagram/identifier .ext" "GET https://reactome.org/ContentService/exporter/document/event/ identifier.pdf"
Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815.
Other "Reactome Content Service - Format Exporter":
rba_reactome_exporter_event(),
rba_reactome_exporter_overview(),
rba_reactome_exporter_reaction()
## Not run:
rba_reactome_exporter_diagram(event_id = "R-HSA-177929",
create_document = FALSE)
## End(Not run)
## Not run:
rba_reactome_exporter_diagram(event_id = "R-HSA-6787403",
create_document = FALSE)
## End(Not run)
## Not run:
rba_reactome_exporter_diagram(event_id = "R-HSA-177929",
create_document = TRUE)
## End(Not run)
## Not run:
rba_reactome_exporter_diagram(event_id = "R-HSA-177929",
output_format = "svg",
save_to = "reactome_event_diagram.svg")
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.