RGraphSpace (version 1.5.2)

normalizeGeometry,GraphSpace-method: Normalize or fit node geometry

Description

Two related operations for keeping an sfc geometry column attached to a GraphSpace's nodes in registration with the node coordinates, for two different situations.

Usage

# S4 method for GraphSpace
normalizeGeometry(gs, name = "geometry", verbose = TRUE)
# S4 method for GraphSpace
fitGeometry(gs, name = "geometry", use_node_size = TRUE, verbose = TRUE)

Value

The updated GraphSpace object.

Arguments

gs

A GraphSpace object.

name

Character. Name of the geometry column to operate on.

verbose

Logical. Whether to report progress messages.

use_node_size

Logical. If TRUE (the default), fitGeometry() also rescales each geometry to match its node's nodeSize. If FALSE, only repositioning happens, each feature keeps its current size.

Details

normalizeGeometry is for geometry that is already spatially meaningful, with its own coordinates genuinely correspond to the nodes (e.g. real cell-segmentation boundaries) and only needs realigning to the current, normalized node frame. It fits a linear regression between the geometry's centroids and the node coordinates and rescales the geometry accordingly, warning if the fit is poor (the geometry did not, in fact, scale linearly with the nodes).

fitGeometry is for geometry that is not yet spatially related to the nodes, as arbitrary shapes used for node markers. It repositions every shape so its centroid sits exactly at its node's coordinates and, when use_node_size = TRUE, also rescales each shape so its diameter matches nodeSize.

Both require gs to already be normalized (see normalizeGraphSpace), and both operate on a single named geometry column, leaving any other geometry columns untouched.

Examples

if (FALSE) {
# Mode 1: geometry already spatially meaningful, just needs realigning
gs_geometry(gs, "geometry") <- real_cell_boundaries
gs <- normalizeGeometry(gs)

# Mode 2: arbitrary shapes, sized and positioned like nodes
gs_geometry(gs, "geometry") <- arbitrary_shapes
gs <- fitGeometry(gs, use_node_size = TRUE)
}