CographLayout R6 Class

Class for managing layout algorithms and computing node positions.

Value

A CographLayout R6 object.

Methods

Public methods

• CographLayout$new()

• CographLayout$compute()

• CographLayout$normalize_coords()

• CographLayout$get_type()

• CographLayout$get_params()

• CographLayout$print()

• CographLayout$clone()

---

Method new()

Create a new CographLayout object.

Usage

CographLayout$new(type = "circle", ...)

Arguments

type

Layout name. One of the names returned by list_layouts(), or "custom" together with a coords argument.

...

Additional parameters stored and passed to the layout function.

Returns

A new CographLayout object.

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Method compute()

Compute layout coordinates for a network.

Usage

CographLayout$compute(network, ...)

Arguments

network

A CographNetwork or cograph_network object.

...

Additional parameters passed to the layout function. They override parameters given to $new().

Returns

A data frame with columns x and y, one row per node, rescaled by $normalize_coords().

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Method normalize_coords()

Rescale coordinates into the unit square. Both axes are scaled by the same factor, so the larger spread spans [padding, 1 - padding] and the layout is centered at 0.5.

Usage

CographLayout$normalize_coords(coords, padding = 0.1)

Arguments

coords

Matrix or data frame. Columns x and y are used, or the first two columns when these names are absent.

padding

Numeric. Margin left on each side of the larger spread.

Returns

A data frame with rescaled x and y columns.

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Method get_type()

Get layout type.

Usage

CographLayout$get_type()

Returns

A character string.

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Method get_params()

Get layout parameters.

Usage

CographLayout$get_params()

Returns

A list of the parameters given to $new().

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Method print()

Print layout summary.

Usage

CographLayout$print()

Returns

The object itself, invisibly.

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Method clone()

The objects of this class are cloneable with this method.

Usage

CographLayout$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

layout <- CographLayout$new("circle")
layout$compute(CographNetwork$new(regulation_net))
#>            x         y
#> 1  0.7351141 0.8236068
#> 2  0.8804226 0.6236068
#> 3  0.8804226 0.3763932
#> 4  0.7351141 0.1763932
#> 5  0.5000000 0.1000000
#> 6  0.2648859 0.1763932
#> 7  0.1195774 0.3763932
#> 8  0.1195774 0.6236068
#> 9  0.2648859 0.8236068
#> 10 0.5000000 0.9000000