PathwaySpace: Spatial projection of network signals along geodesic paths

PathwaySpace is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices. The package processes the signal using a convolution algorithm that considers the graph's topology to project the signal on a 2D space.

PathwaySpace could have various applications, such as visualizing network data in a graphical format that highlights the relationships and signal strengths between vertices.

Installation in R (>=4.4)

Install dependencies to build the package's vignettes

install.packages("knitr")
install.packages("rmarkdown")

Install the PathwaySpace package

install.packages("remotes")
remotes::install_github("sysbiolab/RGraphSpace", build_vignettes=TRUE)
remotes::install_github("sysbiolab/PathwaySpace", build_vignettes=TRUE)

Examples

Follow the PathwaySpace vignette and try to make some brain plots!

library(PathwaySpace)
vignette("PathwaySpace")

Citation

If you use PathwaySpace, please cite:

• Tercan et al. A protocol to assess pathway space distances between classifier feature sets (under review, 2025).

• Ellrott et al. Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets. Cancer Cell, 2025. DOI: 10.1016/j.ccell.2024.12.002

Supporting Material for Tercan et al. (2025)

Download and uncompress Tercan_et_al_20250112.zip, then follow the instructions in the pspace_perturbation.R script. This R script has been developed to reproduce the results presented in Figure S1 of Tercan et al. (2025).

• Tercan_et_al_20250112.zip

Licenses

The PathwaySpace package is distributed under Artistic-2.0