From c63e1d3082999d9cb9f37f054a9d2dfb560229c4 Mon Sep 17 00:00:00 2001 From: William Ryan Date: Thu, 30 May 2024 02:58:38 -0400 Subject: [PATCH] Add additional information regarding PAVER --- README.Rmd | 44 ++++++++++++++-- README.md | 79 ++++++++++++++++++++++++++--- man/figures/README-hunter_plot.jpg | Bin 0 -> 33520 bytes man/figures/README-pressure-1.png | Bin 3744 -> 0 bytes man/figures/README-theme_plot.jpg | Bin 0 -> 15822 bytes vignettes/PAVER.Rmd | 2 +- 6 files changed, 113 insertions(+), 12 deletions(-) create mode 100644 man/figures/README-hunter_plot.jpg delete mode 100644 man/figures/README-pressure-1.png create mode 100644 man/figures/README-theme_plot.jpg diff --git a/README.Rmd b/README.Rmd index 4d18a37..951904d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,6 +20,10 @@ knitr::opts_chunk$set( 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: @@ -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: [William.Ryan2@rockets.utoledo.edu](mailto:William.Ryan2@rockets.utoledo.edu) +- **Ali Sajid Imami** - E-mail: [Ali.Imami@rockets.utoledo.edu](mailto:Ali.Imami@rockets.utoledo.edu) +- **Hunter Eby** - E-mail: [Hunter.Eby@rockets.utoledo.edu](mailto:Hunter.Eby@rockets.utoledo.edu) +- **John Vergis** - E-mail: [John.Vergis@utoledo.edu](mailto:John.Vergis@utoledo.edu) +- **Xiaolu Zhang** - E-mail: [xiaolu.zhang@lsuhs.edu](mailto:xiaolu.zhang@lsuhs.edu) +- **Jarek Meller** - E-mail: [mellerj@ucmail.uc.edu](mailto:mellerj@ucmail.uc.edu) +- **Rammohan Shukla** - E-mail: [rshukla@uwyo.edu](mailto:rshukla@uwyo.edu) +- **Robert McCullumsmith** - E-mail: [robert.mccullumsmith@utoledo.edu](mailto: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](https://github.com/willgryan/PAVER/issues). For technical questions, please contact [William.Ryan2@rockets.utoledo.edu](mailto:William.Ryan2@rockets.utoledo.edu). + +For the corresponding author, please contact [robert.mccullumsmith@utoledo.edu](mailto:robert.mccullumsmith@utoledo.edu). ## 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. - diff --git a/README.md b/README.md index ad2b12c..dead234 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,16 @@ 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 . 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 @@ -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 . 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. + +
+Theme 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_hunter_plot` function. + +
+Heatmap Plot + +
+ +## Authors + +- **William G Ryan V** - E-mail: +- **Ali Sajid Imami** - E-mail: +- **Hunter Eby** - E-mail: +- **John Vergis** - E-mail: +- **Xiaolu Zhang** - E-mail: +- **Jarek Meller** - E-mail: +- **Rammohan Shukla** - E-mail: +- **Robert McCullumsmith** - E-mail: + +## 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 . + +For the corresponding author, please contact +. ## Contributing diff --git a/man/figures/README-hunter_plot.jpg b/man/figures/README-hunter_plot.jpg new file mode 100644 index 0000000000000000000000000000000000000000..f389f51ee02a82287355fdfdc5cdb4825a02f31a GIT binary patch literal 33520 zcmb@t2UwF&w=WvHiWoXl0|KH{L5fO=NEZ=NdW%X2L!<`@M37zu1Qdi=sM4e(Ez+e) zZ=oh2N>8YPgmB~kJ9~f6-uFDuzV|$5g$e7OcQWs+nR#c{`mHsmQ>Tjn*1Ng}x&Rs) z06?Gm0i0q1w{_rd&H#Xs5kL|E0Gt8PM7aUzsT{QkfRCC00NM|<|B*wJ_JQs{dEvh| zPjR%j4Yaf%4;~up8r;+Qr)t`3n%Z}CXjuUOsHd;@L%ln~mR8onOheS#nE@Pt>j2d! z4nEH{A3V7Cw+2s`r_a zY0v!SpZ<#%_{;k`!T&xNpapv#=>MN{p?bf zdHesbD;nDC0Korr{qH*7UjzV*^8f&P^1t&G699k@(f|N3?caHqrcJI&Yt7uxyZ{W zep%wmRY^r9WtAH@Z)s`k=<4Yk+nyN|D*e*ir2#jEg$$f)R; z*p$>aY3Uhn-(`OKoSTc>e~Cr?{+DF`O)fU7T(tD`bo5Mr<)Wbtpe8ytdIk}B zMs`gTrYBw;mlQ(JaNbG&SkZb`^!h_Q*HiD|bKGKzSaHH%(f*O_|C?Z8|3{Mjr(pk< zYX+bNp#6vFXldyf=;-Je7#XOAG4 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--git a/vignettes/PAVER.Rmd b/vignettes/PAVER.Rmd index af0c5ef..5e622f3 100644 --- a/vignettes/PAVER.Rmd +++ b/vignettes/PAVER.Rmd @@ -86,7 +86,7 @@ PAVER_regulation_plot(PAVER_result) ## 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)