exportImage: Image exporter

In reactome/ReactomeContentService4R: Interface for the Reactome Content Service

Image exporter

Description

The diagram exporter allows researchers to include images of their favorite pathway diagrams into their publications, posters or presentations. For details see Reactome diagram exporter guide.

Usage

exportImage(
  id = NULL,
  output = c("diagram", "fireworks", "reaction"),
  species = NULL,
  format = c("png", "jpg", "jpeg", "svg", "gif"),
  quality = 5,
  flg = NULL,
  flgInteractors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  ehld = TRUE,
  diagramProfile = "Modern",
  token = NULL,
  resource = "TOTAL",
  analysisProfile = "Standard",
  expColumn = NULL,
  fireworksCoverage = FALSE,
  file = NULL,
  ...
)

Arguments

id	stable or db id of a ReactionLikeEvent for "reaction" output, or id of an Event for "diagram"
output	type of exported image including "diagram", "fireworks", "reaction"
species	name or db id or taxon id of a species. Used in "fireworks" output
format	output format including "png", "jpg", "jpeg", "svg", "gif"
quality	result image quality between 1-10, default is 5
flg	gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
flgInteractors	defines whether to take into account interactors for the flagging
sel	highlight element(s) selection in the diagram
title	whether the name of the pathway is shown below
margin	defines the image margin between 0-20, default is 15
ehld	whether textbook-like illustration are taken into account
diagramProfile	color profile, "modern" or "standard"
token	token from Reactome Analysis Service
resource	the analysis resource for which the results will be overlaid on top of the given pathways overview
analysisProfile	analysis color profile including "Standard", "Strosobar", "Copper%20plus"
expColumn	the specific expression analysis results column to be overlaid. If it is not specified (null), the first one is selected. If it is not specified (null) and format is gif, then an animated gif is generated with all the columns.
fireworksCoverage	set TRUE to overlay analysis coverage values in a fireworks image
file	full path of the output file
...	additional parameters passed to magick::image_write()

Value

an image saved into the specified path or a magick image object. More magick processing see the package.

See Also

magick to further process the image object

Other exporter: exportEventFile()

Examples

# fireworks
exportImage(species="9606", output="fireworks", 
            format="jpg", quality=7)

## Not run: 
# animated gifs of EHLDs
# can use your own token from your Reactome Analysis
gif <- exportImage(id="R-HSA-69278", output="diagram", format="gif",
                   sel="R-HSA-69242", token="MjAyMDA2MTcyMDM5NDBfMzU2")
print(gif)

# reaction
exportImage(id="R-HSA-6787403", output="reaction", format="svg",
       flg="MTO1", analysisProfile="Copper%20plus", file="R-HSA-6787403.svg")


## End(Not run)

reactome/ReactomeContentService4R documentation built on May 1, 2023, 5:33 a.m.