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Add additional information regarding PAVER
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44 changes: 41 additions & 3 deletions README.Rmd
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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/](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](https://cdrl-ut.org/project/projects_and_posters/paver/).

## Installation

You can install the development version of PAVER from [GitHub](https://github.com/) with:
Expand All @@ -30,11 +34,45 @@ if (!requireNamespace("remotes", quietly = TRUE))
remotes::install_github("willgryan/PAVER")
```

## Usage
## Download

Alternatively, you may download the latest package release for PAVER [here](https://github.com/willgryan/PAVER/releases/latest). You may also download the latest release of the R Shiny app for the PAVER R package [here](https://github.com/willgryan/PAVER_shiny/releases/latest).

Pre-computed pathway embeddings for use with PAVER are available for download here [here](https://github.com/willgryan/PAVER_embeddings).

## 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.

![Theme Plot](man/figures/README-theme_plot.jpg)

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/](https://cdrl.shinyapps.io/PAVER/). For more detailed information on PAVER and its functionalities, please refer to the article on the Cognitive Disorders Research Laboratory (CDRL) website [here](https://cdrl-ut.org/project/projects_and_posters/paver/).
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.

![Heatmap Plot](man/figures/README-hunter_plot.jpg)

## Authors

- **William G Ryan V** - E-mail: [[email protected]](mailto:[email protected])
- **Ali Sajid Imami** - E-mail: [[email protected]](mailto:[email protected])
- **Hunter Eby** - E-mail: [[email protected]](mailto:[email protected])
- **John Vergis** - E-mail: [[email protected]](mailto:[email protected])
- **Xiaolu Zhang** - E-mail: [[email protected]](mailto:[email protected])
- **Jarek Meller** - E-mail: [[email protected]](mailto:[email protected])
- **Rammohan Shukla** - E-mail: [[email protected]](mailto:[email protected])
- **Robert McCullumsmith** - E-mail: [[email protected]](mailto:[email protected])

## 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](https://github.com/willgryan/PAVER/issues). For technical questions, please contact [[email protected]](mailto:[email protected]).

For the corresponding author, please contact [[email protected]](mailto:[email protected]).

## 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](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

79 changes: 71 additions & 8 deletions README.md
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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](https://cdrl-ut.org/project/projects_and_posters/paver/).

## Installation

You can install the development version of PAVER from
Expand All @@ -20,15 +30,68 @@ if (!requireNamespace("remotes", quietly = TRUE))
remotes::install_github("willgryan/PAVER")
```

## Usage
## Download

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 refer to the article on the
Cognitive Disorders Research Laboratory (CDRL) website
[here](https://cdrl-ut.org/project/projects_and_posters/paver/).
Alternatively, you may download the latest package release for PAVER
[here](https://github.com/willgryan/PAVER/releases/latest). You may also
download the latest release of the R Shiny app for the PAVER R package
[here](https://github.com/willgryan/PAVER_shiny/releases/latest).

Pre-computed pathway embeddings for use with PAVER are available for
download here [here](https://github.com/willgryan/PAVER_embeddings).

## 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.

<figure>
<img src="man/figures/README-theme_plot.jpg" alt="Theme Plot" />
<figcaption aria-hidden="true">Theme Plot</figcaption>
</figure>

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.

<figure>
<img src="man/figures/README-hunter_plot.jpg" alt="Heatmap Plot" />
<figcaption aria-hidden="true">Heatmap Plot</figcaption>
</figure>

## Authors

- **William G Ryan V** - E-mail: <[email protected]>
- **Ali Sajid Imami** - E-mail: <[email protected]>
- **Hunter Eby** - E-mail: <[email protected]>
- **John Vergis** - E-mail: <[email protected]>
- **Xiaolu Zhang** - E-mail: <[email protected]>
- **Jarek Meller** - E-mail: <[email protected]>
- **Rammohan Shukla** - E-mail: <[email protected]>
- **Robert McCullumsmith** - E-mail: <[email protected]>

## 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](https://github.com/willgryan/PAVER/issues). For technical
questions, please contact <[email protected]>.

For the corresponding author, please contact
<[email protected]>.

## Contributing

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2 changes: 1 addition & 1 deletion vignettes/PAVER.Rmd
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## Heatmap Plot

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_heatmap_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.

```{r}
PAVER_hunter_plot(PAVER_result)
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