plotGraphSpace,GraphSpace-method {RGraphSpace}R Documentation

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)


[Package RGraphSpace version 1.0.9 Index]