pathwayspace
PathwaySpace is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices.
Science Score: 39.0%
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○CITATION.cff file
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✓DOI references
Found 7 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Keywords
Repository
PathwaySpace is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices.
Basic Info
- Host: GitHub
- Owner: sysbiolab
- Language: R
- Default Branch: main
- Homepage: https://sysbiolab.github.io/PathwaySpace/
- Size: 13.8 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
PathwaySpace: Spatial projection of network signals along geodesic paths
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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.
Figure 1 illustrates the convolution operation problem addressed by
the PathwaySpace package. For detailed documentation and usage examples,
see the package's vignette and workflows.
PathwaySpace could have various applications, such as visualizing network data in a graphical format that highlights the relationships and signal strengths between vertices.
Figure 1. Signal processing addressed by the PathwaySpace package. A) Graph overlaid on a 2D coordinate system. Each projection cone represents the signal associated with a graph vertex (referred to as vertex-signal positions), while question marks indicate positions with no signal information (referred to as null-signal positions). Inset: Graph layout of a toy example used in the package's vignette. B) Illustration of signal projection from two neighboring vertices, simplified to one dimension. Right: Signal profiles from aggregation and decay functions.
Installation in R (>=4.4)
Install dependencies to build the package's vignettes
r
install.packages("knitr")
install.packages("rmarkdown")
Install the PathwaySpace package
r
install.packages("remotes")
remotes::install_github("sysbiolab/RGraphSpace", build_vignettes=TRUE)
remotes::install_github("sysbiolab/PathwaySpace", build_vignettes=TRUE)
Vignette
r
library(PathwaySpace)
vignette("PathwaySpace")
Tutorials
Citation
If you use PathwaySpace, please cite:
Tercan & Apolonio et al. Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods. STAR Protocols, 2025. https://doi.org/10.1016/j.xpro.2025.103681
Ellrott et al. Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets. Cancer Cell, 2025. https://doi.org/10.1016/j.ccell.2024.12.002
Supporting Material for Tercan et al. (2025)
Download and uncompress Tercanetal_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).
Licenses
The PathwaySpace package is distributed under Artistic-2.0
Owner
- Name: Bioinformatics and Systems Biology Laboratory
- Login: sysbiolab
- Kind: organization
- Location: Curitiba, Brazil
- Website: http://www.bioinfo.ufpr.br
- Repositories: 2
- Profile: https://github.com/sysbiolab
GitHub Events
Total
- Watch event: 1
- Delete event: 1
- Push event: 55
- Fork event: 1
- Create event: 1
Last Year
- Watch event: 1
- Delete event: 1
- Push event: 55
- Fork event: 1
- Create event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mauro Castro | m****o@g****m | 46 |
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 7 months
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 7 months
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- vapolonio (1)
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- cran 278 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
cran.r-project.org: PathwaySpace
Spatial Projection of Network Signals along Geodesic Paths
- Homepage: https://github.com/sysbiolab/PathwaySpace
- Documentation: http://cran.r-project.org/web/packages/PathwaySpace/PathwaySpace.pdf
- License: Artistic-2.0
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Latest release: 1.0.2
published 7 months ago