Skip to content

README.md

Latest commit

 

History

History
71 lines (53 loc) · 3.27 KB

README.md

File metadata and controls

71 lines (53 loc) · 3.27 KB

RGraphSpace: A lightweight interface between 'igraph' and 'ggplot2' graphics

RGraphSpace is an R package that generates ggplot2 graphics for igraph objects, scaling nodes and edges to a unit space. The package implements new ggplot2 prototypes, optimized for representing large networks. This enables extensive customization of aesthetics and visual style, including colors, shapes, and line types. Three specialized geoms translate graph data into geometric layers. These geoms use a dual-anchor normalization approach to align layers, required for analysis where network elements must be accurately referenced to a spatial map.

  1. geom_graphspace(): A high-level convenience layer that processes both nodes and edges in a single call.
  2. geom_nodespace(): Dedicated to rendering nodes. Inherits GeomPoint aesthetic mappings, modified to inform the edge layer on node states.
  3. geom_edgespace(): Handles the relational data between nodes. Inherits GeomSegment aesthetic mappings; unlike standard segments, it is "node-aware" and dynamically calibrates start and end points to connected nodes.

By scaling graph elements, RGraphSpace also supports the overlay of networks onto image features. Its dual-anchor normalization approach aligns nodes with matrix indices, which is critical for pixel-level precision.

RGraphSpace may provide infrastructure support for packages that require graph data abstraction. For example, it currently provides classes and methods inherited by PathwaySpace, a tool for exploring signal patterns in spatial transcriptomics.

Installation in R (>=4.5)

Install dependencies to build the package's vignettes
install.packages("knitr")
install.packages("rmarkdown")
Install the RGraphSpace package
install.packages("remotes")
remotes::install_github("sysbiolab/RGraphSpace", build_vignettes=TRUE)

Examples

Follow the RGraphSpace vignette and try to make some plots!

library(RGraphSpace)
vignette("RGraphSpace")

Citation

If you use RGraphSpace, please cite:

  • Sysbiolab Team. "RGraphSpace: A lightweight interface between igraph and ggplot2 graphics". R package, 2023. Doi: 10.32614/CRAN.package.RGraphSpace

  • Castro MAA, Wang X, Fletcher MNC, Meyer KB, Markowetz F. "RedeR: R/Bioconductor package for representing modular structures nested networks and multiple levels of hierarchical associations". Genome Biology 13:R29, 2012. Doi: 10.1186/gb-2012-13-4-r29

Licenses

The RGraphSpace package is distributed under Artistic-2.0