Type: Package
Version: 1.0.9
Title: A Lightweight Interface Between 'ggplot2' and 'igraph' Objects
Description: Interface to integrate 'igraph' and 'ggplot2' graphics within spatial maps. 'RGraphSpace' implements new geometric objects using 'ggplot2' prototypes, customized for representing large 'igraph' objects in a normalized coordinate system. By scaling shapes and graph elements, 'RGraphSpace' can provide a framework for layered visualizations.
Depends: R(≥ 4.4), methods, ggplot2
Imports: grDevices, scales, grid, igraph, lifecycle
Suggests: knitr, rmarkdown, testthat
Enhances: RedeR
License: Artistic-2.0
VignetteBuilder: knitr
URL: https://github.com/sysbiolab/RGraphSpace
BugReports: https://github.com/sysbiolab/RGraphSpace/issues
Collate: gspaceChecks.R gspaceValidation.R gspaceSupplements.R gspaceMisc.R gspacePlots.R gspaceClasses.R gspaceGenerics.R gspaceMethods.R
Encoding: UTF-8
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-07-23 18:16:03 UTC; maac
Author: Victor Apolonio [ctb], Vinicius Chagas [ctb], Mauro Castro ORCID iD [aut, cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Repository: CRAN
Date/Publication: 2025-07-23 19:10:25 UTC

RGraphSpace: A lightweight package for representing large igraph objects in a normalized coordinate system

Description

RGraphSpace is an R package that integrates igraph and ggplot2 graphics within spatial maps. RGraphSpace implements new geometric objects using ggplot2 protypes, customized for representing large igraph objects in a normalized coordinate system. By scaling shapes and graph elements, RGraphSpace can provide a framework for layered visualizations.

Details

Package: RGraphSpace
Type: Software
License: GPL-3
Maintainer: Mauro Castro mauro.a.castro@gmail.com

Index

GraphSpace: Constructor of GraphSpace-class objects.
plotGraphSpace: Plotting igraph objects with RGraphSpace package.
getGraphSpace: Accessors for fetching slots from a GraphSpace object.

Further information is available in the vignettes by typing vignette('RGraphSpace'). Documented topics are also available in HTML by typing help.start() and selecting the RGraphSpace package from the menu.

Author(s)

Maintainer: Mauro Castro mauro.a.castro@gmail.com (ORCID)

Other contributors:

References

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.

See Also

Useful links:

Constructor of GraphSpace-class objects

Description

GraphSpace is a constructor of GraphSpace-class objects.

Usage

GraphSpace(g, mar = 0.1, layout = NULL, image = NULL, verbose = TRUE)

Arguments

g

An igraph object. It must include graph coordinates assigned to x and y vertex attributes, and vertex labels assigned to name vertex attribute.

mar

A single numeric value (in [0,1]) indicating the size of the outer margins as a fraction of the graph space. Note: When an image is provided, mar is a fraction of image margins.

layout

An optional numeric matrix with two columns for x and y coordinates.

image

An optional background image. When provided, x and y coordinates must represent pixel positions in the image space.

verbose

A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

A GraphSpace class object.

Author(s)

Sysbiolab.

See Also

plotGraphSpace

Examples

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')

gs <- GraphSpace(gtoy1)

GraphSpace: An S4 class for igraph objects

Description

GraphSpace: An S4 class for igraph objects

Value

An S4 class object.

Slots

nodes

A data frame with xy-vertex coordinates.

edges

A data frame with edges.

graph

An igraph object.

image

A raster background image matrix.

pars

A list with parameters.

misc

A list with intermediate objects for downstream methods.

Constructor

see GraphSpace constructor.

Accessors for fetching slots from a GraphSpace object

Description

getGraphSpace retrives information from individual slots available in a GraphSpace object.

Usage

## S4 method for signature 'GraphSpace'
getGraphSpace(gs, what = "graph")

Arguments

gs

A preprocessed GraphSpace class object

what

A single character value specifying which information should be retrieved from the slots. Options: 'graph','gxy','gxyz','pars','misc','status','summits', 'summit_mask', and 'summit_contour'.

Value

Content from slots in the GraphSpace object.

Examples

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')

# Create a new GraphSpace object
gs <- GraphSpace(gtoy1)

# Get the 'summary' slot in gs
getGraphSpace(gs, what = 'graph')

Toy 'igraph' objects

Description

Small 'igraph' objects used for workflow demonstrations. All graphs include 'x', 'y', and 'name' vertex attributes.

Usage

data(gtoy1)

Format

igraph

Value

A pre-processed igraph object.

Source

This package.

Examples

data(gtoy1)
data(gtoy2)

Accessors for applying essential igraph methods to modify attributes of GraphSpace objects.

Description

Access and modify individual slots of a GraphSpace object. Selected 'igraph' methods are applied to the 'graph' slot and propagated to downstream components.

Usage

## S4 method for signature 'GraphSpace'
names(x)

## S4 replacement method for signature 'GraphSpace'
names(x) <- value

## S4 method for signature 'GraphSpace'
gs_vcount(x)

## S4 method for signature 'GraphSpace'
gs_ecount(x)

## S4 method for signature 'GraphSpace'
gs_vertex_attr(x, name, ...)

## S4 replacement method for signature 'GraphSpace'
gs_vertex_attr(x, name, ...) <- value

## S4 method for signature 'GraphSpace'
gs_edge_attr(x, name, ...)

## S4 replacement method for signature 'GraphSpace'
gs_edge_attr(x, name, ...) <- value

Arguments

x

A GraphSpace class object

value

The new value of the attribute.

name

Name of the attribute.

...

Additional arguments passed to igraph methods.

Value

Updated GraphSpace object.

See Also

vertex_attr, edge_attr

Examples

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')

# Create a new GraphSpace object
gs <- GraphSpace(gtoy1)

# Usage of GraphSpace attribute accessors:

# Get vertex names
names(gs)

# Get vertex count
gs_vcount(gs)

# Get edge count
gs_ecount(gs)

# Access all vertex attributes
gs_vertex_attr(gs)

# Access a specific vertex attribute
gs_vertex_attr(gs, "nodeLabel")

# Modify a single value within a vertex attribute
gs_vertex_attr(gs, "nodeSize")["n1"] <- 10

# Replace an entire vertex attribute
gs_vertex_attr(gs, "nodeSize") <- 10

# Alternative syntax using `$` accessor
gs_vertex_attr(gs)$nodeSize <- 10

# Access a specific edge attribute
gs_edge_attr(gs, "edgeLineColor")

# Replace an entire edge attribute
gs_edge_attr(gs, "edgeLineWidth") <- 1

 # Alternative syntax using `$` for edge attributes
gs_edge_attr(gs)$edgeLineWidth <- 3

Plot GraphSpace objects

Description

Plot GraphSpace objects

Usage

## S3 method for class 'GraphSpace'
plot(x, ...)

Arguments

x

A GraphSpace class object.

...

Additional arguments passed to the plotGraphSpace function.

See Also

plotGraphSpace

Plotting igraph objects with RGraphSpace

Description

plotGraphSpace is a wrapper function to create dedicated ggplot graphics for igraph- and GraphSpace-class objects.

Usage

## S4 method for signature 'GraphSpace'
plotGraphSpace(
  gs,
  theme = c("th0", "th1", "th2", "th3"),
  xlab = "Graph coordinates 1",
  ylab = "Graph coordinates 2",
  font.size = 1,
  bg.color = "grey95",
  add.labels = FALSE,
  node.labels = NULL,
  label.size = 3,
  label.color = "grey20",
  add.image = FALSE,
  marks = deprecated(),
  mark.size = deprecated(),
  mark.color = deprecated()
)

## S4 method for signature 'igraph'
plotGraphSpace(gs, ..., mar = 0.1)

Arguments

gs

Either an igraph or GraphSpace class object. If gs is an igraph, then it must include x, y, and name vertex attributes (see GraphSpace).

theme

Name of a custom RGraphSpace theme. These themes (from 'th1' to 'th3') consist of preconfigured ggplot settings, which the user can subsequently refine using ggplot2.

xlab

The title for the 'x' axis of a 2D-image space.

ylab

The title for the 'y' axis of a 2D-image space.

font.size

A single numeric value passed to ggplot themes.

bg.color

A single color for background.

add.labels

A logical value indicating whether to plot vertex labels.

node.labels

A vector of vertex names to be highlighted in the graph space. This argument overrides 'add.labels'.

label.size

A size argument passed to geom_text.

label.color

A color passed to geom_text.

add.image

A logical value indicating whether to add a background image, when one is available (see GraphSpace).

marks

Deprecated from RGraphSpace 1.0.9; use 'node.labels' instead.

mark.size

Deprecated from RGraphSpace 1.0.9; use 'label.size' instead.

mark.color

Deprecated from RGraphSpace 1.0.9; use 'label.color' instead.

...

Additional arguments passed to the plotGraphSpace function.

mar

A single numeric value (in [0,1]) indicating the size of the outer margins as a fraction of the graph space.

Value

A ggplot-class object.

Author(s)

Sysbiolab.

See Also

GraphSpace

Examples

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')

# Generate a ggplot for igraph
plotGraphSpace(gtoy1)

# Create a GraphSpace object
gs <- GraphSpace(gtoy1)

# Generate a ggplot for gs
plotGraphSpace(gs)