ggraph: Create a ggraph plot

In YTLogos/ggraph: An Implementation of Grammar of Graphics for Graphs and Networks

Description

This function is the equivalent of ggplot in ggplot2. It takes care of setting up the plot object along with creating the layout for the plot based on the graph and the specification passed in. Alternatively a layout can be prepared in advance using create_layout and passed as the data argument. See Details for a desciption of all available layouts.

Usage

ggraph(graph, layout = "auto", ...)

create_layout(graph, layout, circular, ...)

## Default S3 method:
create_layout(graph, layout, ...)

## S3 method for class 'dendrogram'
create_layout(graph, layout, circular = FALSE, ...)

## S3 method for class 'igraph'
create_layout(graph, layout, circular = FALSE, ...)

## S3 method for class 'hclust'
create_layout(graph, layout, circular = FALSE, ...)

## S3 method for class 'network'
create_layout(graph, layout, circular = FALSE, ...)

Arguments

graph	The object containing the graph. See Details for a list of supported classes. Or a layout_ggraph object as returned from create_layout in which case all subsequent arguments is ignored.
layout	The type of layout to create.
...	Arguments passed on to the layout function.
circular	Should the layout be transformed into a radial representation. Only possible for some layouts. Defaults to FALSE

Details

Following is a short description of the different layout types available in ggraph. Each layout is further described in its own help pages.

Dendrogram objects

The dendrogram class is used to store binary tree from e.g. hierarchical clustering. The layouts provided for this class is constrained to tree-like representations. hclust objects are supported through automatic conversion to dendrogram objects and thus supports the same layouts.

auto

The default layout. Eqivalent to layout = 'dendrogram'

dendrogram

Creates a tree using the heights already defined in the dendrogram object. See layout_dendrogram_dendrogram for further details

even

Ignores the heights given by the dendrogram object and instead spreads the branch points out with an even distance. See layout_dendrogram_even for further details

Further, if the layouts provided for igraph objects are needed for dendrogram objects den_to_igraph is provided to convert dendrograms to igraph.

igraph objects

Any type of regular graph/network data can be represented as an igraph object. Because of this the different layouts that can be applied to igraph objects are quite diverse, but not all layouts makes sense to all types of graphs. It is up to the user to understand their data and choose an appropriate layout. For standard node-edge diagrams igraph itself defines a long range of different layout functions that are all available through the igraph layout where the specific layout is specified using the algorithm argument. In order to minimize typing all igraph algorithms can also be passed directly into the layout argument. network objects are supported by automatic conversion to igraph objects using network_to_igraph and thus supports the same layouts.

auto

The default layout. Equivalent to layout = 'igraph', algorithm = 'nicely'

igraph

Use one of the internal igraph layout algorithms. The algorithm is specified using the algorithm argument. All strings accepted by the algorithm argument can also be supplied directly into layout. See layout_igraph_igraph for further details

dendrogram

Lays out the nodes in a tree-like graph as a dendrogram with leaves set at 0 and parents 1 unit above its tallest child. See layout_igraph_dendrogram for further details

manual

Lets the user manually specify the location of each node by supplying a data.frame with an x and y column. See layout_igraph_manual for further details

linear

Arranges the nodes linearly or circularly in order to make an arc diagram. See layout_igraph_linear for further details

treemap

Creates a treemap from the graph, that is, a space-filing subdivision of rectangles showing a weighted hierarchy. See layout_igraph_treemap for further details

circlepack

Creates a layout showing a hierarchy as circles within circles. Conceptually equal to treemaps. See layout_igraph_circlepack for further details

partition

Create icicle or sunburst charts, where each layer subdivides the division given by the preceeding layer. See layout_igraph_partition for further details

hive

Positions nodes on axes spreading out from the center based on node attributes. See layout_igraph_hive for further details

Value

For ggraph() an object of class gg onto which layers, scales, etc. can be added. For create_layout() an object inherting from layout_ggraph. layout_ggraph itself inherits from data.frame and can be considered as such. The data.frame contains the node positions in the x and y column along with additional columns generated by the specific layout, as well as node parameters inherited from the graph. Additional information is stored as attributes to the data.frame. The original graph object is stored in the graph attribute and the circular attribute contains a logical indicating whether the layout has been transformed to a circular representation.

See Also

get_edges for extracting edge information from the layout and get_con for extracting path information.

Examples

require(igraph)
gr <- make_graph('bull')
layout <- create_layout(gr, layout = 'igraph', algorithm = 'kk')

YTLogos/ggraph documentation built on May 6, 2019, 4:37 p.m.