| 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. |
| Authors: | Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [aut, cre] |
| Maintainer: | Mauro Castro <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.0.7 |
| Built: | 2024-11-12 03:17:03 UTC |
| Source: | https://github.com/sysbiolab/rgraphspace |
getGraphSpace retrives information from
individual slots available in a GraphSpace object.
## S4 method for signature 'GraphSpace' getGraphSpace(gs, what = "summary")## S4 method for signature 'GraphSpace' getGraphSpace(gs, what = "summary")
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'. |
Content from slots in the GraphSpace object.
# 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 = 'summary')# 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 = 'summary')
GraphSpace is a constructor of
GraphSpace-class objects.
GraphSpace(g, layout = NULL, mar = 0.075, verbose = TRUE)GraphSpace(g, layout = NULL, mar = 0.075, verbose = TRUE)
g |
An |
layout |
an optional numeric matrix with two columns for |
mar |
A single numeric value (in |
verbose |
A single logical value specifying to display detailed
messages (when |
A GraphSpace class object.
Sysbiolab.
# Load a demo igraph data('gtoy1', package = 'RGraphSpace') gs <- GraphSpace(gtoy1)# Load a demo igraph data('gtoy1', package = 'RGraphSpace') gs <- GraphSpace(gtoy1)
GraphSpace: An S4 class for PathwaySpace graphics
An S4 class object.
nodesA data frame with xy-vertex coordinates.
edgesA data frame with edges.
graphAn igraph object.
parsA list with parameters.
miscA list with intermediate objects for downstream methods.
see GraphSpace constructor.
Small 'igraph' objects used for workflow demonstrations. All graphs include 'x', 'y', and 'name' vertex attributes.
data(gtoy1)data(gtoy1)
igraph
A pre-processed igraph object.
This package.
data(gtoy1) data(gtoy2)data(gtoy1) data(gtoy2)
plotGraphSpace is a wrapper function to
create dedicated ggplot graphics for igraph- and GraphSpace-class objects.
## S4 method for signature 'GraphSpace' plotGraphSpace( gs, xlab = "Graph coordinates 1", ylab = "Graph coordinates 2", font.size = 1, theme = c("th1", "th2", "th3"), bg.color = "grey95", marks = FALSE, mark.size = 3, mark.color = "grey20" ) ## S4 method for signature 'igraph' plotGraphSpace(gs, ..., layout = NULL, mar = 0.075)## S4 method for signature 'GraphSpace' plotGraphSpace( gs, xlab = "Graph coordinates 1", ylab = "Graph coordinates 2", font.size = 1, theme = c("th1", "th2", "th3"), bg.color = "grey95", marks = FALSE, mark.size = 3, mark.color = "grey20" ) ## S4 method for signature 'igraph' plotGraphSpace(gs, ..., layout = NULL, mar = 0.075)
gs |
Either an |
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. |
theme |
Name of a custom RGraphSpace theme. These themes (from 'th1' to 'th3') consist mainly of preconfigured ggplot settings, which the user can subsequently fine-tune within the resulting ggplot object. |
bg.color |
A single color for background. |
marks |
A logical value indicating whether to add 'marks' to vertex positions. Alternatively, this could be a vector listing vertex names. |
mark.size |
A font size argument passed to |
mark.color |
A color passed to |
... |
Additional arguments passed to the
|
layout |
an optional numeric matrix with two columns for |
mar |
A single numeric value (in |
A ggplot-class object.
Sysbiolab.
# Load a demo igraph data('gtoy1', package = 'RGraphSpace') # Generate a ggplot for gtoy1 plotGraphSpace(gtoy1) # Create a GraphSpace object gs <- GraphSpace(gtoy1) # Generate a ggplot for gs plotGraphSpace(gs)# Load a demo igraph data('gtoy1', package = 'RGraphSpace') # Generate a ggplot for gtoy1 plotGraphSpace(gtoy1) # Create a GraphSpace object gs <- GraphSpace(gtoy1) # Generate a ggplot for gs plotGraphSpace(gs)