PAVER: Pathway Analysis Visualization with Embedding Representations

PAVER allows for summary interpretation and visualization of pathway analyses.

Usage

PAVER is designed to work with the output of pathway analysis tools. The package includes a vignette with an example dataset that explains it’s functionality. The R Shiny application for the PAVER R package is hosted at https://cdrl.shinyapps.io/PAVER/. For more detailed information on PAVER and its functionalities, please read further below and also refer to the article on the Cognitive Disorders Research Laboratory (CDRL) website here.

Downloads

You may download the latest source release for PAVER here. You may also download the latest release of the R Shiny app for the PAVER R package here.

Pre-computed pathway embeddings for use with PAVER are available for download here.

Installation

You can install the development version of PAVER from GitHub with:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("willgryan/PAVER")

Example

PAVER offers different visualizations for exploring and interpreting pathway clusters.

The theme plot is a scatter plot showing all pathways in the dataset, colored by theme. The theme plot is useful for identifying pathways that are similar to each other, and for identifying pathways that are outliers. The theme plot can be generated using the PAVER_theme_plot function.

The heatmap plot shows the enrichment scores for each pathway in each cluster. The heatmap plot is useful for quantitatively identifying identifying differences in pathway regulation across different pathway analyses. The heatmap plot can be generated using the PAVER_hunter_plot function.

Authors

William G Ryan V - E-mail: William.Ryan2@rockets.utoledo.edu
Ali Sajid Imami - E-mail: Ali.Imami@rockets.utoledo.edu
Hunter Eby - E-mail: Hunter.Eby@rockets.utoledo.edu
John Vergis - E-mail: John.Vergis@utoledo.edu
Xiaolu Zhang - E-mail: xiaolu.zhang@lsuhs.edu
Jarek Meller - E-mail: mellerj@ucmail.uc.edu
Rammohan Shukla - E-mail: rshukla@uwyo.edu
Robert McCullumsmith - E-mail: robert.mccullumsmith@utoledo.edu

Acknowledgements

PAVER was supported by NIH NIGMS T32-G-RISE grant number 1T32GM144873-01, NIH NIMH grant number R01MH107487, NIH NIMH grant number R01MH121102, and NIH NIA grant number R01AG057598.

Contact

For technical issues, please start a new issue on this repository. For technical questions, please contact William.Ryan2@rockets.utoledo.edu.

For the corresponding author, please contact robert.mccullumsmith@utoledo.edu.

Citation

If you use PAVER in your work, please cite the following article:

Interpreting and visualizing pathway analyses using embedding representations with PAVER
Ryan et al. Bioinformation 20(7): 700-704 (2024)

Contributing

We welcome anyone wishing to contribute, report issues or seek support for PAVER. Please note, PAVER is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.