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Normalize node coordinates to graph and image spaces

Source: R/gspace-normalize.R
normalizeGraphSpace-methods.Rd

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 class 'GraphSpace'
normalizeGraphSpace(
  gs,
  mar = 0.1,
  image.space = .has_image(gs),
  flip.x = FALSE,
  flip.y = image.space,
  flip.v = FALSE,
  flip.h = FALSE,
  swap.xy = FALSE,
  verbose = TRUE,
  rotate.xy = deprecated(),
  use_image = deprecated()
)

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

Arguments

gs

A GraphSpace object to be normalized.

mar

A single numeric value in [0, 0.5] controlling the size of the outer margins around the graph. Without an image, mar specifies symmetric margins as a fraction of the graph space. With an image, mar is interpreted as a fraction of the available image margins surrounding the graph.

image.space

Logical; if an image is available, whether to use it as a background reference map. When enabled, x and y graph coordinates are interpreted as pixel coordinates in the image matrix. Images can be inspected and assigned with gs_image.

flip.x

Logical; whether to flip the node coordinates along the x-axis.

flip.y

Logical; whether to flip the node coordinates along the y-axis. Useful for aligning nodes with image backgrounds, which often use an inverted coordinate system. Defaults to image.space.

flip.v

Logical; whether to vertically flip the background image matrix (top-to-bottom) to align with the graph coordinate system.

flip.h

Logical; whether to horizontally flip the background image matrix (left-to-right) to align with the graph coordinate system.

swap.xy

Logical; whether to swap x and y node coordinates. Useful when the graph coordinate system is transposed relative to the image or reference map.

verbose

A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

rotate.xy

Deprecated from RGraphSpace 1.4.3; use swap.xy instead.

use_image

Deprecated from RGraphSpace 1.4.0; use image.space instead.

crop.coord

An optional numeric vector of length four specifying a cropping region (xmin, xmax, ymin, ymax), with values in normalized coordinates [0,1].

Value

A GraphSpace object with updated nodes and image slots.

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 image.space = FALSE) or maps them to pixel coordinates (when image.space = TRUE and an image is provided; see gs_image). It handles image-to-graph alignment via flip.\* and swap.\* 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.

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)
#> Validating the 'igraph' object...
#> Vertex attributes 'x' and 'y' missing; computing layout...
#> Vertex attribute 'name' missing; assigning names... 
#> Ignoring graph-level attributes: 'name', 'loops'
#> Creating a 'GraphSpace' object...

gs <- normalizeGraphSpace(gs)
#> Normalizing node coordinates to graph space...

gs_crop <- cropGraphSpace(gs, crop.coord = c(0, 1, 0, 0.5))

plotGraphSpace(gs, add.labels = TRUE)


plotGraphSpace(gs_crop, add.labels = TRUE)