Package {RGraphSpace}

Type:	Package
Version:	1.4.0
Title:	A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics
Description:	An interface to integrate 'igraph' and 'ggplot2' graphics within a normalized coordinate system. 'RGraphSpace' extends 'ggplot2' with graph-aware geometries optimized for large networks. The 'GraphSpace' class integrates directly with 'ggplot2' through specialized 'geoms' and lazy resolution of node attributes, supporting customization of aesthetics and visual styles. These 'geoms' use a dual-anchor normalization approach to align layers, particularly useful for analyses in which network elements must be spatially aligned with reference maps and images.
Depends:	R(≥ 4.5), methods, ggplot2 (≥ 4.0)
Imports:	grDevices, grid, igraph, tidygraph, scales, rlang, ggrastr, Matrix, lifecycle
Suggests:	knitr, rmarkdown, testthat, ggraph, ggnewscale, patchwork, Seurat, SeuratObject
Enhances:	RedeR
License:	Artistic-2.0
VignetteBuilder:	knitr
URL:	https://github.com/sysbiolab/RGraphSpace, https://sysbiolab.github.io/RGraphSpace/
BugReports:	https://github.com/sysbiolab/RGraphSpace/issues
Collate:	'geom-edgespace.R' 'geom-graphspace.R' 'geom-nodespace.R' 'gspace-checks.R' 'gspace-classes.R' 'gspace-constructor.R' 'gspace-generics.R' 'gspace-methods.R' 'gspace-misc.R' 'gspace-normalize.R' 'gspace-supplements.R' 'gspace-themes.R' 'gspace-validation.R' 'gspace-ggplot-constructor.R' 'annotation-gspace.R' 'gspace-coercion.R' 'gspace-features.R'
Encoding:	UTF-8
Config/roxygen2/version:	8.0.0
NeedsCompilation:	no
Packaged:	2026-06-12 21:32:39 UTC; maac
Author:	Sysbiolab Team [aut], Flávio Kessler [ctb], Jonathan Back [ctb], Lana Querne [ctb], Victor Apolonio [ctb], Vinicius Chagas [ctb], Mauro Castro [cre]
Maintainer:	Mauro Castro <mauro.a.castro@gmail.com>
Repository:	CRAN
Date/Publication:	2026-06-13 05:10:23 UTC

RGraphSpace: A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics

Description

An interface to integrate 'igraph' and 'ggplot2' graphics within a normalized coordinate system. 'RGraphSpace' extends 'ggplot2' with graph-aware geometries optimized for large networks. The 'GraphSpace' class integrates directly with 'ggplot2' through specialized 'geoms' and lazy resolution of node attributes, supporting customization of aesthetics and visual styles. These 'geoms' use a dual-anchor normalization approach to align layers, particularly useful for analyses in which network elements must be spatially aligned with reference maps and images.

Index

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)

Authors:

• Sysbiolab Team

Other contributors:

• Flávio Kessler [contributor]

• Jonathan Back [contributor]

• Lana Querne [contributor]

• Victor Apolonio [contributor]

• Vinicius Chagas [contributor]

References

Sysbiolab Team (2026). RGraphSpace: A lightweight interface between 'igraph' and 'ggplot2' graphics. R package version 1.4.0 (Doi: 10.32614/CRAN.package.RGraphSpace), https://CRAN.R-project.org/package=RGraphSpace.

See Also

Useful links:

• https://github.com/sysbiolab/RGraphSpace

• https://sysbiolab.github.io/RGraphSpace/

• Report bugs at https://github.com/sysbiolab/RGraphSpace/issues

Generate a unique identifier for GraphSpace objects

Description

This helper function creates a unique ID without relying on the R Random Number Generator (RNG), making it immune to set.seed(). It combines the Process ID (PID), high-precision system time, and a system-level temporary identifier to ensure uniqueness across parallel processes and rapid sequential calls.

Usage

.generate_gs_uuid()

Value

A character string containing a unique alphanumeric ID.

GeomEdgeSpace: a ggplot2 prototype for GraphSpace-class methods

Description

GeomEdgeSpace is the underlying ggproto object used by geom_edgespace to draw edge elements in a graph layout.

This geom is designed for network diagrams, where graph attributes are often already in their final form (e.g., hex colors).

Usage

GeomEdgeSpace

Aesthetics

GeomEdgeSpace understands ggplot2's conventions for segment-like geoms.

See Also

geom_edgespace, geom_segment

GeomGraphSpace: a ggplot2 prototype for GraphSpace-class methods

Description

GeomGraphSpace is the underlying ggproto object used by geom_graphspace to draw node and edge elements in a graph layout.

This geom is designed for network diagrams, where graph attributes are often already in their final form (e.g., hex colors).

Usage

GeomGraphSpace

Aesthetics

GeomGraphSpace understands ggplot2's conventions for point-like geoms.

See Also

geom_graphspace, geom_point

GeomNodeSpace: a ggplot2 prototype for GraphSpace-class methods

Description

GeomNodeSpace is the underlying ggproto object used by geom_nodespace to draw node elements in a graph layout.

This geom is designed for network diagrams, where graph attributes are often already in their final form (e.g., hex colors).

Usage

GeomNodeSpace

Aesthetics

GeomNodeSpace understands ggplot2's conventions for point-like geoms.

See Also

geom_nodespace, geom_point

Create a GraphSpace object

Description

GraphSpace is the main constructor for GraphSpace objects, designed to store graph data and metadata for optimized rendering in RGraphSpace.

Usage

## S4 method for signature 'ANY'
GraphSpace(g, layout = NULL, verbose = TRUE, ...)

## S4 method for signature 'data.frame'
GraphSpace(g, verbose = TRUE, ...)

Arguments

Details

GraphSpace objects are designed to bridge the gap between network analysis (via igraph) and high-quality visualization (via ggplot2). The constructor ensures that all necessary aesthetics for geom_graphspace are pre-processed and validated.

Coordinate System and Normalization: By default, the constructor expects coordinates in the x and y vertex attributes, along with unique IDs in the name vertex attribute. If these are not provided, the constructor will generate sequential IDs and assign a layout using the layout_nicely function. These coordinates define the relative positioning of nodes. For optimal rendering, it is recommended to pass the object through normalizeGraphSpace after construction. This converts vertex positions to Normalized Parent Coordinates (NPC), ensuring the graph remains centered and scaled relative to the plotting area.

Data Structure: The resulting object stores nodes and edges in separate internal slots, preserving metadata such as nodeSize and edgeLineColor. If an igraph object is provided without specific styling attributes, GraphSpace will assign the default values defined in the geom_graphspace aesthetics. Users can also specify custom variables in the input graph to be used as aesthetics within the ggplot2 grammar.

Arrowhead Mapping: The arrowType attribute (see Arrowhead types section) allows for a mapping between symbolic aliases (such as "-->") and internal integer codes. This is useful for assigning interaction types in directed or undirected graphs (e.g., activation vs. inhibition).

Value

A GraphSpace class object.

Vertex attributes

The following attributes in g are evaluated by the constructor:

Edge attributes

The following attributes in g are evaluated by the constructor:

Arrowhead types

Arrowheads are controlled via the arrowType attribute using integer or character codes (see examples in the RGraphSpace vignette).

In directed graphs, arrows follow the edge list orientation by default, representing forward directions (e.g., A -> B). While undirected graphs do not show arrows by default, specific styles can be manually assigned for detailed visualization, including forward, backward, or bidirectional arrowheads.

Directed graphs (A -> B):

Undirected graphs (A – B):

Author(s)

Sysbiolab.

See Also

geom_graphspace, plotGraphSpace

Examples

library(RGraphSpace)
library(igraph)

# Create a star graph
gtoy1 <- make_full_graph(15)

# Custom attributes
V(gtoy1)$nodeSize <- 5
E(gtoy1)$edgeLineColor <- "red"
E(gtoy1)$arrowType <- "-->"

# Create a GraphSpace
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 containing node coordinates, attributes, and metadata.

edges

A data frame containing edge relationships and attributes.

graph

An igraph object representing the graph structure.

image

A raster object (see as.raster) used as background image.

fdata

A Matrix object storing high-dimensional feature data associated with graph nodes.

pars

A list with parameters.

misc

A list with intermediate objects for downstream methods.

uuid

A Universally Unique Identifier (UUID) for the object instance.

Constructor

see GraphSpace constructor.

Internal methods for GraphSpace

Description

Exported solely to enable RStudio auto-completion and should not be called directly by the user.

Usage

## S3 method for class 'GraphSpace'
.DollarNames(x, pattern = "")

Arguments

Attribute Processing for GeomEdgeSpace

Description

Manage visual attribute precedence (color, size, shape) for GeomEdgeSpace objects.

Usage

StatEdgeSpace

Format

A ggproto object.

Attribute Priority

1. Explicit aes() mappings.

2. Fixed geom_edgespace() arguments.

3. Original graph attributes (via optional_aes).

During the setup_data stage, the Stat invokes internal functions to resolve value priority:

1. Explicit Mapping: Values defined by the user inside aes().

2. Fixed Parameters: Constant values passed as arguments in the geom_edgespace() call.

3. Graph Attributes: Original attributes stored within the GraphSpace object, retrieved from the data columns.

See Also

geom_edgespace

Attribute Processing for GeomNodeSpace

Description

Manage visual attribute precedence (color, size, shape) for GeomNodeSpace objects.

Usage

StatNodeSpace

Format

A ggproto object.

Attribute Priority

1. Explicit aes() mappings.

2. Fixed geom_nodespace() arguments.

3. Original graph attributes (via optional_aes).

During the setup_data stage, the Stat invokes internal functions to resolve value priority:

1. Explicit Mapping: Values defined by the user inside aes().

2. Fixed Parameters: Constant values passed as arguments in the geom_nodespace() call.

3. Graph Attributes: Original attributes stored within the GraphSpace object, retrieved from the data columns.

See Also

geom_nodespace

Annotate a GraphSpace Plot

Description

annotation_gspace() is a generic dispatcher for adding annotation layers to a ggplot-based GraphSpace plot. The type argument selects the annotation type; additional arguments are forwarded to the corresponding handler.

Usage

annotation_gspace(..., type = "image")

annotation_gspace_image(
  raster,
  interpolate = FALSE,
  opacity = 1,
  flip.v = FALSE,
  flip.h = FALSE
)

Arguments

Value

A ggplot2 layer object that can be added to a ggplot() call with +, or invisible(NULL) with a warning if the image could not be resolved.

See Also

annotation_raster, gs_image, geom_nodespace, geom_edgespace

Examples

# Assuming 'gs' is a GraphSpace object with 
# an image stored in gs_image(gs)

## Not run: 
# Pass a GraphSpace object directly
ggplot(gs) +
  annotation_gspace(gs) +
  geom_edgespace() +
  geom_nodespace()

# Extract the image explicitly
ggplot(gs) +
  annotation_gspace(gs_image(gs)) +
  geom_edgespace() +
  geom_nodespace()

# Dim the background and flip vertically
ggplot(gs) +
  annotation_gspace(gs, opacity = 0.5, flip.v = TRUE) +
  geom_edgespace() +
  geom_nodespace()
  

## End(Not run)

Convert objects to GraphSpace

Description

S3 generic function for coercing objects into a GraphSpace object.

Usage

as.GraphSpace(x, ...)

## Default S3 method:
as.GraphSpace(x, ...)

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

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

## S3 method for class 'data.frame'
as.GraphSpace(x, ...)

## S3 method for class 'Seurat'
as.GraphSpace(x, space = c("embedding", "spatial"), layer = NULL, ...)

Arguments

Details

Unified entry point for converting graph, spatial, and high-dimensional data into a GraphSpace object.

Graph objects are imported either through native methods or via as_tbl_graph when available.

For Seurat objects, coordinate extraction depends on the selected space:

• space = "embedding" uses the first two dimensions returned by Embeddings.

• space = "spatial" uses tissue coordinates returned by GetTissueCoordinates.

Assay data are stored in the data slot of the resulting GraphSpace object. Node metadata from x@meta.data are appended to the node table.

Value

A GraphSpace object.

See Also

GraphSpace

Map numeric values to a color raster

Description

Helper function that converts numeric values to colors and returns a raster image. Useful for visualizing numeric matrices as color backgrounds.

Usage

as_colorraster(x, palette = hcl.colors(30), na.color = "white")

Arguments

Details

Values in x are rescaled to the range of the palette using scales::rescale(), and each value is mapped to a corresponding color. If x is a matrix, the resulting raster preserves the same dimensions.

Value

A raster object as produced by as.raster().

Examples

library(RGraphSpace)

# Convert the volcano matrix to a color raster
img <- as_colorraster(volcano)
plot(img)

Draw edge elements in a 2D graph layout

Description

Constructor for GeomEdgeSpace ggproto objects.

A wrapper around geom_segment that enables direct use of edge attributes stored in GraphSpace objects as aesthetics.

This geom is designed to create edge-level aesthetics such as colour and linewidth, or any custom aesthetics defined in GeomEdgeSpace.

Usage

geom_edgespace(
  mapping = NULL,
  data = NULL,
  stat = StatEdgeSpace,
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  arrow_size = 1,
  arrow_offset = 0.01,
  lineend = "butt",
  linejoin = "mitre",
  raster = FALSE,
  dpi = NULL,
  dev = "cairo",
  scale = 1
)

edgespace_handler()

Arguments

Details

arrow_size is a numeric scaling factor controlling arrowhead geometry. The value is interpreted in the same numeric space as line width (lwd), ensuring consistent scaling between edge strokes and arrowheads.

arrow_offset is an additive term that offsets arrow endpoints uniformly in graph space and is bounded by the edge length, in NPC units.

Arrowhead types are specified in the GraphSpace constructor.

Value

A ggplot2 layer that renders edge segments defined by GeomEdgeSpace.

Aesthetics

geom_edgespace() understands geom_segment aesthetics.

If these aesthetics are not explicitly provided in aes(), they are automatically retrieved from the GraphSpace object.

Required aesthetics (x, y, xend, yend, ...) are supplied from the GraphSpace object and do not need to be manually mapped.

Additional parameters can be passed to control fixed values for the layer. For example: colour = "grey", linetype = 2, linewidth = 1.

Arrows can be further adjusted by arrow_size and arrow_offset arguments (see details).

Integration with ggraph

geom_edgespace is compatible with the ggraph methods. When used within a ggraph() call, the default edgespace_handler() automatically:

• Identifies the current layout_ggraph.

• Extracts the x and y coordinates calculated by ggraph.

• Reconstructs a temporary GraphSpace object to inject spatial metadata and user-chosen ggraph layout.

See Also

GraphSpace, geom_nodespace, geom_graphspace, geom_segment

Examples

library(RGraphSpace)
library(igraph)
library(ggplot2)

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

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

## Not run: 

ggplot() +
  geom_edgespace(data = gs) +
  geom_nodespace(data = gs) +
  theme(aspect.ratio = 1)


## End(Not run)

Draw node and edge elements in a 2D graph layout

Description

Constructor for GeomGraphSpace ggproto objects.

A wrapper around geom_point that enables direct use of node attributes stored in GraphSpace objects as aesthetics.

This geom is designed to map node-level attributes (e.g., fill, size) or any aesthetics supported by GeomPoint.

Usage

geom_graphspace(
  mapping = NULL,
  data,
  stat = "identity",
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  arrow_size = 1,
  arrow_offset = 0.01,
  raster = FALSE,
  dpi = NULL,
  dev = "cairo",
  scale = 1
)

Arguments

Value

A ggplot2 layer that renders node glyphs defined by GeomGraphSpace.

Aesthetics for node drawing

Nodes are drawn in the main layer of geom_graphspace(), which understands geom_point aesthetics.

If these aesthetics are not explicitly provided in aes(), they are automatically retrieved from the GraphSpace object.

Required aesthetics x, y, and vertex are supplied from the GraphSpace object and do not need to be manually mapped.

Additional parameters can be passed to control fixed values for the layer. For example: fill = "red", stroke = 3, alpha = 0.5, or shape = 21.

The interpretation of size depends on how it is provided:

• As an aesthetic: When mapped within aes(), size follows the behavior of geom_point, using absolute units to ensure consistency with the plot legends.

• As a parameter: When set outside aes(), size is treated as a percentage of the viewport ([0, 100]), scaling in npc units. This allows nodes to resize dynamically with viewport changes.

Edge context-aware parameters

These parameters control the edge appearance. If not explicitly provided, they are automatically retrieved from the GraphSpace object. They can be a single value or a vector matching the number of edges:

Edge global parameters

These parameters apply globally to all edges in the layer:

arrow_size is a numeric scaling factor controlling arrowhead geometry. The value is interpreted in the same numeric space as line width (lwd), ensuring consistent scaling between edge strokes and arrowheads.

arrow_offset is an additive term that offsets arrow endpoints uniformly in graph space and is bounded by the edge length, in NPC units.

Arrowhead types are specified in the GraphSpace constructor.

See Also

GraphSpace, geom_nodespace, geom_edgespace, geom_point

Examples

library(RGraphSpace)
library(igraph)
library(ggplot2)

# Make a demo igraph
gtoy1 <- make_star(15, mode="out")

# Set some node attributes
V(gtoy1)$nodeSize <- runif(vcount(gtoy1), 1, 20)
V(gtoy1)$nodeColor <- rainbow(vcount(gtoy1))

# Set some variables
V(gtoy1)$user_var1 <- runif(vcount(gtoy1), 1, 3)^3
V(gtoy1)$user_var2 <-  rep(c(1, 2, 3), each = 5)

# Create a GraphSpace object
gs <- GraphSpace(gtoy1, layout = layout_in_circle(gtoy1))

## Not run: 

# Example 1: Nodes scaling with the legend
# When 'size' is mapped inside aes(), it follows
# ggplot2 default behavior: size is translated 
# to absolute units (mm) via 'scale_size()'.

ggplot() + 
  geom_graphspace(
  mapping = aes(size = nodeSize, fill = user_var2), 
  data = gs, arrow_offset = 0.01) + 
  scale_size(range = c(1, 12)) + 
  theme(aspect.ratio = 1)
  
# Example 2: Nodes scaling with the viewport
# When 'size' is passed as a node attribute, 
# inherited from the igraph object, it is
# interpreted as a percentage of the plotting 
# area and translated to NPC units.

ggplot() +
  geom_graphspace(mapping = aes(fill = user_var2), 
  data = gs, arrow_offset = 0.01) + 
  theme(aspect.ratio = 1)
  

## End(Not run)

Draw node elements in a 2D graph layout

Description

Constructor for GeomNodeSpace ggproto objects.

A wrapper around geom_point that enables direct use of node attributes stored in GraphSpace objects as aesthetics.

This geom is designed to map node-level attributes (e.g., fill, size) or any aesthetics supported by GeomPoint.

Usage

geom_nodespace(
  mapping = NULL,
  data = NULL,
  stat = StatNodeSpace,
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  raster = FALSE,
  dpi = NULL,
  dev = "cairo",
  scale = 1
)

nodespace_handler(mapping = NULL)

Arguments

Details

The interpretation of size depends on how it is provided:

• As an aesthetic: When mapped within aes(), size follows the behavior of geom_point, using absolute units to ensure consistency with the plot legends.

• As a parameter: When set outside aes(), size is treated as a percentage of the viewport ([0, 100]), scaling in npc units. This allows nodes to resize dynamically with viewport changes.

Value

A ggplot2 layer that renders node glyphs defined by GeomNodeSpace.

Aesthetics

geom_nodespace() understands geom_point aesthetics.

If these aesthetics are not explicitly provided in aes(), they are automatically retrieved from the GraphSpace object.

Required aesthetics x and y are supplied from the GraphSpace object and do not need to be manually mapped.

Additional parameters can be passed to control fixed values for the layer. For example: fill = "red", stroke = 3, alpha = 0.5, or shape = 21.

Integration with ggraph

geom_nodespace is compatible with the ggraph methods. When used within a ggraph() call, the default nodespace_handler() automatically:

• Identifies the current layout_ggraph.

• Extracts the x and y coordinates calculated by ggraph.

• Reconstructs a temporary GraphSpace object to inject spatial metadata and user-chosen ggraph layout.

See Also

GraphSpace, geom_edgespace, geom_graphspace, geom_point

Examples

library(RGraphSpace)
library(igraph)
library(ggplot2)

# Make a demo igraph
gtoy1 <- make_star(15, mode="out")

# Set some node attributes
V(gtoy1)$nodeSize <- runif(vcount(gtoy1), 1, 20)
V(gtoy1)$nodeColor <- rainbow(vcount(gtoy1))

# Set some variables
V(gtoy1)$user_var1 <- runif(vcount(gtoy1), 1, 3)^3
V(gtoy1)$user_var2 <-  rep(c(1, 2, 3), each = 5)

# Create a GraphSpace object
gs <- GraphSpace(gtoy1, layout = layout_in_circle(gtoy1))

## Not run: 

# Example 1: Nodes scaling with the legend
# When 'size' is mapped inside aes(), it follows
# ggplot2 default behavior: size is translated 
# to absolute units (mm) via 'scale_size()'.

ggplot() + 
geom_edgespace(data = gs, arrow_offset = 0.01) +
  geom_nodespace(mapping = aes(size = nodeSize, fill = user_var2), 
  data = gs) + 
  scale_size(range = c(1, 12)) + 
  theme(aspect.ratio = 1)
  
# Example 2: Nodes scaling with the viewport
# When 'size' is passed as a node attribute, 
# inherited from the igraph object, it is 
# interpreted as a percentage of the plotting 
# area and translated to NPC units.

ggplot() + 
geom_edgespace(data = gs, arrow_offset = 0.01) +
geom_nodespace(mapping = aes(fill = user_var2), data = gs) +
theme(aspect.ratio = 1)
  

## End(Not run)

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

Value

Content from slots in the GraphSpace object.

Examples

library(RGraphSpace)
library(igraph)

# 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')

Using ggplot2 with GraphSpace objects

Description

GraphSpace objects can be used directly with ggplot2, allowing node attributes and high-dimensional feature data to be mapped through standard aesthetic mappings without manual data extraction. This integration enables:

• Lazy evaluation of node attributes and feature data.

• Automatic synchronization of node metadata for standard ggplot2 geoms such as geom_point.

• Automatic propagation of node metadata required for edge clipping and arrow placement in GraphSpace-native geoms.

Usage

## S3 method for class 'GraphSpace'
ggplot(data, mapping = NULL, ...)

Arguments

Details

When a GraphSpace object is supplied to ggplot(), RGraphSpace extends the standard ggplot2 build process to automatically resolve GraphSpace variables and synchronize node metadata required for edge rendering.

When using ggplot(), neither nodespace_handler nor inject_nodespace need to be called explicitly.

Value

A gspace_plot object extending ggplot.

See Also

GraphSpace, geom_nodespace, geom_edgespace, inject_nodespace, nodespace_handler, edgespace_handler

Examples

library(RGraphSpace)
library(igraph)
library(ggplot2)

# Generate a toy star graph
gtoy1 <- make_star(15, mode = "out")
V(gtoy1)$my_node_var <- runif(vcount(gtoy1), 1, 20)

# Create a GraphSpace object
gs <- GraphSpace(gtoy1, layout = layout_in_circle(gtoy1))

## Not run: 

# Example 1: Using RGraphSpace-native geoms
# Edge clipping metadata are injected automatically
ggplot(gs) +
  geom_edgespace(colour = "red") +
  geom_nodespace(aes(size = my_node_var), 
  fill = "steelblue", stroke = 2) +
  scale_size(range = c(2, 15))

# Example 2: Mixing native and general geoms
# Note possible clipping mismatch when combining
# geom_edgespace() with generic ggplot2 node geoms.
# Since geom_point() does not expose the final rendered
# node radius to RGraphSpace, edge clipping is estimated
# from layer parameters and may not exactly match the
# displayed node geometry.
ggplot(gs) +
  geom_edgespace(colour = "red") +
  geom_point(aes(x, y, size = my_node_var), 
  fill = "steelblue", stroke = 2, shape = 21) +
  scale_size(range = c(2, 15))


## End(Not run)

Manipulate node features in a GraphSpace object

Description

Utilities for extracting and adding node-associated features stored in the fdata container of a GraphSpace object.

Usage

gs_fetch_features(x, vars = NULL, as_df = FALSE)

gs_add_features(x, data)

Arguments

Value

• gs_fetch_features() returns a matrix-like object or data.frame containing the selected node features.

• gs_add_features() returns a modified GraphSpace object.

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

library(RGraphSpace)
data(gtoy1)
data(gtoy2)

Dynamic Scale Injection for Edge Clipping

Description

Utility function for RGraphSpace that enables edge layers to scan adjacent nodes and determine their dimensions. This information is used to compute arrow clipping offsets, preventing edge geometry from overlapping node symbols.

Usage

inject_nodespace(...)

Arguments

Details

This function operates in two stages within the ggplot2 workflow:

1. Capture: It scans the plot layers for a GeomNodeSpace to extract both mapping variables (from aes()) and static parameters (specifically size and stroke).

2. Injection: It locates GeomEdgeSpace layers and injects scale rules, captured mappings, and fixed parameters into the geometry parameters.

This "lazy injection" calculates edge clipping based on the actual scales used by the nodes, even if scales are defined after the layers.

Note: inject_nodespace() must be called last in the ggplot chain to allow the function to correctly scan all previously added layers and scales.

Value

An object of class inject_nodespace, which interacts with the ggplot2 + operator.

See Also

geom_edgespace, geom_nodespace

Examples

library(RGraphSpace)
library(igraph)
library(ggplot2)

# Generate a toy star graph
gtoy1 <- make_star(15, mode="out")

# Set node and edge attributes
V(gtoy1)$my_node_var <- runif(vcount(gtoy1), 1, 20)
E(gtoy1)$my_edge_var <-  runif(ecount(gtoy1), 1, 20)

# Create a GraphSpace object with a circular layout
gs <- GraphSpace(gtoy1, layout = layout_in_circle(gtoy1))

## Not run: 
# Build the plot
# Note that inject_nodespace() is called at the end to
# synchronize node sizes with edge clipping.
ggplot() +
  geom_edgespace(aes(colour = my_edge_var), data = gs) +
  geom_nodespace(aes(size = my_node_var), data = gs) +
  scale_size(range = c(2, 15)) +
  inject_nodespace()

## End(Not run)

Accessors and attribute utilities for GraphSpace objects

Description

Access and modify individual components of a GraphSpace object. Selected igraph methods are applied to the internal graph representation and propagated to downstream node and edge components.

Usage

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

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

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

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

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

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

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

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

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

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

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

## 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

## S4 method for signature 'GraphSpace'
x$name

## S4 replacement method for signature 'GraphSpace'
x$name <- value

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

Arguments

Details

For gs_nodes(), the optional vars argument specifies node-associated features retrieved from the fdata container. See also gs_fetch_features.

Value

Updated GraphSpace object.

See Also

vertex_attr, edge_attr, gs_fetch_features

Examples

library(RGraphSpace)
library(igraph)

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

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

#--- Usage of GraphSpace attribute accessors:

# Vertex names
names(gs)

# Vertex attribute names
gs_names(gs)

# Get a data frame with nodes
gs_nodes(gs)

# Get a data frame with edges
gs_edges(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

# Add an image and rescale graph coordinates to image space
# Images may be provided as a raster or numeric matrix
gs_image(gs) <- as_colorraster(volcano)
gs <- normalizeGraphSpace(gs)

Normalize node coordinates to graph and image spaces

Description

Accessory functions to normalize node coordinates in GraphSpace, either by centering them within the graph boundaries or by mapping them to pixel coordinates of a background image.

Usage

## S4 method for signature 'GraphSpace'
normalizeGraphSpace(
  gs,
  mar = 0.1,
  use_image = FALSE,
  flip.x = FALSE,
  flip.y = FALSE,
  rotate.xy = FALSE,
  flip.v = FALSE,
  flip.h = FALSE,
  verbose = TRUE,
  image = deprecated()
)

## S4 method for signature 'GraphSpace'
cropGraphSpace(gs, crop.coord = c(0, 1, 0, 1), verbose = TRUE)

Arguments

Details

These functions provide different strategies for coordinate transformation:

• normalizeGraphSpace: Re-scales node coordinates to a [0, 1] unit square based on the graph's bounding box (when use_image = FALSE) or maps them to pixel coordinates (when use_image = TRUE and an image is provided; see gs_image). It handles image-to-graph alignment via flip.\* and rotate.\* arguments, used to adjust the graph origin with the image matrix layout. Users should be aware of the potential discrepancy between image matrix orientation (top-down) and graph coordinates (bottom-up). The function attempts to automatically adjust the y-axis to align the graph's bottom-up coordinates with the image's top-down layout, but further manual adjustments might be required.

• cropGraphSpace: Subsets the normalized graph space into a specific region defined by crop.coord. It recalculates node positions and background image boundaries to maintain spatial consistency after cropping. This function requires a previously normalized GraphSpace object.

Value

A GraphSpace object with updated nodes and image slots.

Note

This is an accessory function typically called during the preprocessing of GraphSpace objects before rendering.

See Also

gs_image

Examples

library(RGraphSpace)
library(igraph)

# Create a star graph
gtoy1 <- make_full_graph(30)

# Create a GraphSpace
gs <- GraphSpace(gtoy1)

gs <- normalizeGraphSpace(gs)

gs_crop <- cropGraphSpace(gs, 
         crop.coord = c(0, 0.75, 0, 0.75))

Plot GraphSpace objects

Description

Plot GraphSpace objects

Usage

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

Arguments

See Also

plotGraphSpace

Wrapper function to plot GraphSpace objects in ggplot2

Description

plotGraphSpace() is a High-level plotting interface that translates igraph and GraphSpace data objects into ggplot2 layers.

Usage

## S4 method for signature 'GraphSpace'
plotGraphSpace(
  gs,
  theme = "th0",
  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 = TRUE,
  raster = FALSE,
  dpi = 300,
  dev = "cairo_png"
)

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

## S4 method for signature 'tbl_graph'
plotGraphSpace(gs, ...)

## S4 method for signature 'gs_graph'
plotGraphSpace(gs, ...)

Arguments

Value

A ggplot-class object.

Author(s)

Sysbiolab.

See Also

GraphSpace

Examples

library(RGraphSpace)
library(igraph)

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

# Generate a ggplot for gtoy1
plotGraphSpace(gtoy1)

# Create a star graph
gtoy_star <- make_full_graph(15)

# Example of setting node and edge attributes
V(gtoy_star)$nodeSize <- 5
E(gtoy_star)$edgeLineColor <- "red"
E(gtoy_star)$arrowType <- "<->"

# Create a GraphSpace object
gs_star <- GraphSpace(gtoy_star)

# Normalize graph coordinates
gs_star <- normalizeGraphSpace(gs_star)

# Generate a ggplot for gs_star
plotGraphSpace(gs_star)

RGraphSpace ggplot2 themes

Description

A set of ggplot2 themes used by RGraphSpace plots.

Usage

theme_gspace_th0(
  txt_size = 1,
  leg_size = 1,
  bg_colour = "grey95",
  discrete_fill = FALSE,
  discrete_colour = FALSE,
  ...
)

theme_gspace_th1(
  txt_size = 1,
  leg_size = 1,
  bg_colour = "grey95",
  discrete_fill = FALSE,
  discrete_colour = FALSE,
  ...
)

theme_gspace_th2(
  txt_size = 1,
  leg_size = 1,
  bg_colour = "grey95",
  discrete_fill = FALSE,
  discrete_colour = FALSE,
  ...
)

theme_gspace_th3(
  txt_size = 1,
  leg_size = 1,
  bg_colour = "grey95",
  discrete_fill = FALSE,
  discrete_colour = FALSE,
  ...
)

theme_gspace_coords(
  theme = "th0",
  is_norm = FALSE,
  xlab = "Graph coordinates 1",
  ylab = "Graph coordinates 2",
  expand = NULL,
  ...
)

theme_gspace_legend(
  leg_size = 1,
  discrete_fill = FALSE,
  discrete_colour = FALSE,
  ...
)

Arguments

Details

theme_gspace_th0() is a minimal wrapper around theme_gray that simplifies axis and legend scaling. The txt_size and leg_size arguments aggregate related theme parameters for quick thematic overrides.

theme_gspace_th1() builds on theme_gspace_th0() and modifies grid lines, axis appearance, and panel borders.

theme_gspace_th2() is similar to theme_gspace_th1() with simplified grid elements and a customizable panel background.

theme_gspace_th3() is similar to theme_gspace_th2() but with slightly adjusted margins, tick appearance, and legend formatting.

The theme_gspace_coords() is a helper function that also adds axes scales for normalized coordinates. It configures axis breaks, limits, and expansion for graph layouts. Plot coordinates are ideally normalized to the interval [0, 1].

theme_gspace_legend() is helper function that adjusts legend text, title, and key sizes by a single scaling factor.

Value

theme_gspace_th*() return a ggplot2 theme object.

theme_gspace_coords() returns a list containing scale and theme components that can be added to a ggplot2 plot.

theme_gspace_legend() returns a list of theme and guide components.

See Also

ggtheme, theme

Examples

library(RGraphSpace)
library(ggplot2)

ggplot(mtcars, aes(wt, mpg)) +
  geom_point() +
  theme_gspace_th0()
  
ggplot(mtcars, 
  aes(scales::rescale(wt), 
      scales::rescale(mpg))) +
  geom_point() +
  theme_gspace_coords("th2", is_norm = TRUE)
  
# Reduce legend element sizes
ggplot(mtcars, aes(wt, mpg, fill = factor(cyl))) + 
  geom_point(shape = 21) + 
  theme_gspace_legend(0.8)