Getting Started with RGraphSpace
Sysbiolab Team
2026-09-09
Source:vignettes/articles/get-started.Rmd
get-started.Rmd
Package: RGraphSpace 1.5.4
For a self-contained introduction that works offline, run vignette(“RGraphSpace”) after installing the package.
Introductory vignettes
These tutorials introduce RGraphSpace using simple toy
examples: building a
GraphSpace walks through basic graph conventions; customizing aesthetics
demonstrates how to set up geoms to handle graph data
types; scales and offsets
describes the trade-offs involved in synchronizing node and edge layers;
geometries and nodes demonstrates
how to attach sf geometries to nodes as custom markers, and
GraphSpace accessors
covers graph transformation functions, attribute manipulation, and the
package’s general accessors.
General applications
These tutorials showcase RGraphSpace for general
applications: mapping graphs to
images illustrates the use of images as spatial references; interoperability with ggraph &
sf demonstrates some integration strategies, building a graph
from real-world geographic data and comparing it against
ggraph’s own layout approach; and interactive visualization
demonstrates manual graph layout refinement.
Advanced workflows
These tutorials showcase RGraphSpace applied to real-world
scenarios: high-dimensional
data demonstrates how to integrate high-dimensional feature
data; spatial feature data
shows how to attach those features to spatially-organized data; spatial segmentation1
walks through attaching real cell-segmentation boundaries to a
GraphSpace from a Seurat object; spatial segmentation2
demonstrates how to construct a GraphSpace from a
SpatialExperiment object with integrated tissue images, and
nested geometries extends
this to more complex geometries and high-resolution images.
