CITATION.cff

# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# ------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "RGraphSpace" in publications use:'
type: software
license: Artistic-2.0
title: 'RGraphSpace: Rendering Graphs as Coherent Spatial Objects in ''ggplot2'''
version: 1.5.7
doi: 10.21105/joss.11209
identifiers:
- type: doi
  value: 10.32614/CRAN.package.RGraphSpace
abstract: An interface for rendering 'igraph' objects as 'ggplot2' graphics within
  a normalized coordinate space. 'RGraphSpace' implements new geometries that treat
  a graph as a single coherent object, synchronizing node and edge layers under standard
  aesthetic mappings. Node features are resolved on demand, supporting high-dimensional
  data without expanding node tables. Spatial alignment is available at the pixel
  level, with node coordinates anchored to pixel centers through a half-pixel offset,
  enabling precise node positioning over external reference frames such as images
  and maps. Core functionality builds on 'igraph', 'ggplot2', and 'tidygraph'; optional
  geometry and large raster-background images use 'sf' and 'terra' when installed.
authors:
- family-names: Carazza-Kessler
  given-names: Flávio Gabriel
  orcid: https://orcid.org/0000-0002-5309-8043
- family-names: Back
  given-names: Jonathan André
  orcid: https://orcid.org/0009-0008-7338-1197
- family-names: Querne
  given-names: Lana Bazan Peters
  orcid: https://orcid.org/0000-0001-9967-028X
- family-names: Santos
  given-names: Victor Henrique Apolonio
  name-particle: dos
  orcid: https://orcid.org/0000-0002-6394-5840
- family-names: Castro
  given-names: Mauro Antônio Alves
  email: mauro.a.castro@gmail.com
  orcid: https://orcid.org/0000-0003-4942-8131
preferred-citation:
  type: article
  title: 'RGraphSpace: Rendering graphs as coherent spatial objects in ggplot2'
  authors:
  - family-names: Carazza-Kessler
    given-names: Flávio Gabriel
    orcid: https://orcid.org/0000-0002-5309-8043
  - family-names: Back
    given-names: Jonathan André
    orcid: https://orcid.org/0009-0008-7338-1197
  - family-names: Querne
    given-names: Lana Bazan Peters
    orcid: https://orcid.org/0000-0001-9967-028X
  - family-names: Santos
    given-names: Victor Henrique Apolonio
    name-particle: dos
    orcid: https://orcid.org/0000-0002-6394-5840
  - family-names: Castro
    given-names: Mauro Antônio Alves
    email: mauro.a.castro@gmail.com
    orcid: https://orcid.org/0000-0003-4942-8131
  journal: Journal of Open Source Software
  doi: 10.21105/joss.11209
  url: https://doi.org/10.21105/joss.11209
  year: '2026'
  publisher:
    name: The Open Journal
  volume: '11'
  issue: '126'
  start: '11209'
repository: https://CRAN.R-project.org/package=RGraphSpace
repository-code: https://github.com/sysbiolab/RGraphSpace
url: https://sysbiolab.github.io/RGraphSpace/
contact:
- family-names: Castro
  given-names: Mauro Antônio Alves
  email: mauro.a.castro@gmail.com
  orcid: https://orcid.org/0000-0003-4942-8131
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
    website: https://ror.org/02zz1nj61
  institution:
    name: R Foundation for Statistical Computing
    website: https://ror.org/05qewa988
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
  version: '>= 4.5'
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
    website: https://ror.org/02zz1nj61
  institution:
    name: R Foundation for Statistical Computing
    website: https://ror.org/05qewa988
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Depends
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2026'
  doi: 10.32614/CRAN.package.ggplot2
  version: '>= 4.0'
- type: software
  title: igraph
  abstract: 'igraph: Network Analysis and Visualization'
  notes: Imports
  url: https://r.igraph.org/
  repository: https://CRAN.R-project.org/package=igraph
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
    orcid: https://orcid.org/0000-0001-7098-9676
  - family-names: Nepusz
    given-names: Tamás
    email: ntamas@gmail.com
    orcid: https://orcid.org/0000-0002-1451-338X
  - family-names: Traag
    given-names: Vincent
    orcid: https://orcid.org/0000-0003-3170-3879
  - family-names: Horvát
    given-names: Szabolcs
    email: szhorvat@gmail.com
    orcid: https://orcid.org/0000-0002-3100-523X
  - family-names: Zanini
    given-names: Fabio
    email: fabio.zanini@unsw.edu.au
    orcid: https://orcid.org/0000-0001-7097-8539
  - family-names: Noom
    given-names: Daniel
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Schoch
    given-names: David
    email: david.schoch@cynkra.com
    orcid: https://orcid.org/0000-0003-2952-4812
  - family-names: Salmon
    given-names: Maëlle
    email: maelle@cynkra.com
    orcid: https://orcid.org/0000-0002-2815-0399
  year: '2026'
  doi: 10.32614/CRAN.package.igraph
  version: '>= 2.1.0'
- type: software
  title: tidygraph
  abstract: 'tidygraph: A Tidy API for Graph Manipulation'
  notes: Imports
  url: https://tidygraph.data-imaginist.com
  repository: https://CRAN.R-project.org/package=tidygraph
  authors:
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomasp85@gmail.com
    orcid: https://orcid.org/0000-0002-5147-4711
  year: '2026'
  doi: 10.32614/CRAN.package.tidygraph
- type: software
  title: Matrix
  abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
  notes: Imports
  url: https://codeberg.org/jaganmn/Matrix
  repository: https://CRAN.R-project.org/package=Matrix
  authors:
  - family-names: Bates
    given-names: Douglas
    orcid: https://orcid.org/0000-0001-8316-9503
  - family-names: Maechler
    given-names: Martin
    email: mmaechler+Matrix@gmail.com
    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Jagan
    given-names: Mikael
    orcid: https://orcid.org/0000-0002-3542-2938
  year: '2026'
  doi: 10.32614/CRAN.package.Matrix
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
    website: https://ror.org/02zz1nj61
  institution:
    name: R Foundation for Statistical Computing
    website: https://ror.org/05qewa988
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Seidel
    given-names: Dana
  year: '2026'
  doi: 10.32614/CRAN.package.scales
- type: software
  title: ggrastr
  abstract: 'ggrastr: Rasterize Layers for ''ggplot2'''
  notes: Imports
  url: https://github.com/VPetukhov/ggrastr
  repository: https://CRAN.R-project.org/package=ggrastr
  authors:
  - family-names: Petukhov
    given-names: Viktor
    email: viktor.s.petukhov@ya.ru
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    email: t.vd.brand@nki.nl
  - family-names: Biederstedt
    given-names: Evan
    email: evan.biederstedt@gmail.com
  year: '2026'
  doi: 10.32614/CRAN.package.ggrastr
- type: software
  title: gtable
  abstract: 'gtable: Arrange ''Grobs'' in Tables'
  notes: Imports
  url: https://gtable.r-lib.org
  repository: https://CRAN.R-project.org/package=gtable
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.gtable
- type: software
  title: grid
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
    website: https://ror.org/02zz1nj61
  institution:
    name: R Foundation for Statistical Computing
    website: https://ror.org/05qewa988
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
- type: software
  title: grDevices
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
    website: https://ror.org/02zz1nj61
  institution:
    name: R Foundation for Statistical Computing
    website: https://ror.org/05qewa988
    address: Vienna, Austria
  year: '2026'
  doi: 10.32614/R.manuals
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: lifecycle
  abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
  notes: Imports
  url: https://lifecycle.r-lib.org/
  repository: https://CRAN.R-project.org/package=lifecycle
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  year: '2026'
  doi: 10.32614/CRAN.package.lifecycle
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2026'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2026'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.testthat
- type: software
  title: ggraph
  abstract: 'ggraph: An Implementation of Grammar of Graphics for Graphs and Networks'
  notes: Suggests
  url: https://ggraph.data-imaginist.com
  repository: https://CRAN.R-project.org/package=ggraph
  authors:
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomasp85@gmail.com
    orcid: https://orcid.org/0000-0002-5147-4711
  year: '2026'
  doi: 10.32614/CRAN.package.ggraph
- type: software
  title: ggnewscale
  abstract: 'ggnewscale: Multiple Fill and Colour Scales in ''ggplot2'''
  notes: Suggests
  url: https://eliocamp.github.io/ggnewscale/
  repository: https://CRAN.R-project.org/package=ggnewscale
  authors:
  - family-names: Campitelli
    given-names: Elio
    email: eliocampitelli@gmail.com
    orcid: https://orcid.org/0000-0002-7742-9230
  year: '2026'
  doi: 10.32614/CRAN.package.ggnewscale
- type: software
  title: patchwork
  abstract: 'patchwork: The Composer of Plots'
  notes: Suggests
  url: https://patchwork.data-imaginist.com
  repository: https://CRAN.R-project.org/package=patchwork
  authors:
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomasp85@gmail.com
    orcid: https://orcid.org/0000-0002-5147-4711
  year: '2026'
  doi: 10.32614/CRAN.package.patchwork
- type: software
  title: sf
  abstract: 'sf: Simple Features for R'
  notes: Suggests
  url: https://r-spatial.github.io/sf/
  repository: https://CRAN.R-project.org/package=sf
  authors:
  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
    orcid: https://orcid.org/0000-0001-8049-7069
  year: '2026'
  doi: 10.32614/CRAN.package.sf
- type: software
  title: terra
  abstract: 'terra: Spatial Data Analysis'
  notes: Suggests
  url: https://rspatial.org/
  repository: https://CRAN.R-project.org/package=terra
  authors:
  - family-names: Hijmans
    given-names: Robert J.
    email: r.hijmans@gmail.com
    orcid: https://orcid.org/0000-0001-5872-2872
  - family-names: Brown
    given-names: Andrew
    orcid: https://orcid.org/0000-0002-4565-533X
  - family-names: Barbosa
    given-names: Márcia
    orcid: https://orcid.org/0000-0001-8972-7713
  year: '2026'
  doi: 10.32614/CRAN.package.terra
- type: software
  title: SeuratObject
  abstract: 'SeuratObject: Data Structures for Single Cell Data'
  notes: Suggests
  url: https://satijalab.github.io/seurat-object/
  repository: https://CRAN.R-project.org/package=SeuratObject
  authors:
  - family-names: Hoffman
    given-names: Paul
    email: hoff0792@alumni.umn.edu
    orcid: https://orcid.org/0000-0002-7693-8957
  - family-names: Satija
    given-names: Rahul
    email: seurat@nygenome.org
    orcid: https://orcid.org/0000-0001-9448-8833
  - family-names: Collins
    given-names: David
    email: dcollins@nygenome.org
    orcid: https://orcid.org/0000-0001-9243-7821
  - family-names: Hao
    given-names: Yuhan
    email: yhao@nygenome.org
    orcid: https://orcid.org/0000-0002-1810-0822
  - family-names: Hartman
    given-names: Austin
    email: ahartman@nygenome.org
    orcid: https://orcid.org/0000-0001-7278-1852
  - family-names: Molla
    given-names: Gesmira
    email: gmolla@nygenome.org
    orcid: https://orcid.org/0000-0002-8628-5056
  - family-names: Butler
    given-names: Andrew
    email: abutler@nygenome.org
    orcid: https://orcid.org/0000-0003-3608-0463
  - family-names: Stuart
    given-names: Tim
    email: tstuart@nygenome.org
    orcid: https://orcid.org/0000-0002-3044-0897
  year: '2026'
  doi: 10.32614/CRAN.package.SeuratObject
- type: software
  title: SummarizedExperiment
  abstract: 'SummarizedExperiment: A container (S4 class) for matrix-like assays'
  notes: Suggests
  url: https://bioconductor.org/packages/SummarizedExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Morgan
    given-names: Martin
  - family-names: Obenchain
    given-names: Valerie
  - family-names: Hester
    given-names: Jim
  - family-names: Pagès
    given-names: Hervé
    email: hpages.on.github@gmail.com
  year: '2026'
  doi: 10.18129/B9.bioc.SummarizedExperiment
- type: software
  title: SpatialExperiment
  abstract: 'SpatialExperiment: S4 Class for Spatially Resolved -omics Data'
  notes: Suggests
  url: https://github.com/drighelli/SpatialExperiment
  repository: https://bioconductor.org/
  authors:
  - family-names: Righelli
    given-names: Dario
    email: dario.righelli@gmail.com
    orcid: https://orcid.org/0000-0003-1504-3583
  - family-names: Risso
    given-names: Davide
    email: risso.davide@gmail.com
    orcid: https://orcid.org/0000-0001-8508-5012
  - family-names: Crowell
    given-names: Helena L.
    email: helena.crowell@cnag.eu
    orcid: https://orcid.org/0000-0002-4801-1767
  - family-names: Weber
    given-names: Lukas M.
    email: lmweb012@gmail.com
    orcid: https://orcid.org/0000-0002-3282-1730
  year: '2026'
  doi: 10.18129/B9.bioc.SpatialExperiment
- type: software
  title: RedeR
  abstract: 'RedeR: Interactive visualization and manipulation of nested networks'
  notes: Enhances
  url: https://doi.org/10.1186/gb-2012-13-4-r29
  repository: https://bioconductor.org/
  authors:
  - family-names: Castro
    given-names: Mauro
    email: mauro.a.castro@gmail.com
    orcid: https://orcid.org/0000-0003-4942-8131
  year: '2026'
  doi: 10.1186/gb-2012-13-4-r29