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https://github.com/insightsengineering/teal.gallery

A Gallery of Exploratory Web Apps used for Analyzing Clinical Trial Data
https://github.com/insightsengineering/teal.gallery

clinical-trials nest r shiny webapp

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A Gallery of Exploratory Web Apps used for Analyzing Clinical Trial Data

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README 

        
# teal.gallery





  





  




A gallery of sample apps based on the [`teal`](https://github.com/insightsengineering/teal) framework.



## Links to apps on `shinyapps.io`



The Stable version of the apps use the latest released packages while the dev version of the apps use the development packages which are installed from the `main` branch of the respective package repository. The specific versions used can be seen in the `Session Info` of the deployed app.



| Stable version                                    | Dev version                                     |

|---------------------------------------------------|-------------------------------------------------|

| [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_stable/)          | [basic-teal](https://genentech.shinyapps.io/NEST_basic-teal_dev/)         |

| [exploratory](https://genentech.shinyapps.io/NEST_exploratory_stable/)        | [exploratory](https://genentech.shinyapps.io/NEST_exploratory_dev/)       |

| [safety](https://genentech.shinyapps.io/NEST_safety_stable/)                  | [safety](https://genentech.shinyapps.io/NEST_safety_dev/)                 |

| [efficacy](https://genentech.shinyapps.io/NEST_efficacy_stable/)              | [efficacy](https://genentech.shinyapps.io/NEST_efficacy_dev/)             |

| [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_stable/) | [patient-profile](https://genentech.shinyapps.io/NEST_patient-profile_dev/)|

| [early-dev](https://genentech.shinyapps.io/NEST_early-dev_stable/)             | [early-dev](https://genentech.shinyapps.io/NEST_early-dev_dev/)           |

| [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_stable/)       | [longitudinal](https://genentech.shinyapps.io/NEST_longitudinal_dev/)     |

| [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_stable/)                 | [RNA-seq](https://genentech.shinyapps.io/NEST_RNA-seq_dev/)               |

| [python](https://genentech.shinyapps.io/NEST_python_stable/)                   | [python](https://genentech.shinyapps.io/NEST_python_dev/)                 |



## Running the apps



You can run any of these apps by just executing these two lines of code in your R console.



By sourcing the [sourceme.R](https://github.com/insightsengineering/teal.gallery/blob/main/utils/sourceme.R) file you make sure that you have access to the `restore_and_run()`



Note: Make sure to install [renv](https://rstudio.github.io/renv/index.html) before you do this. Also, it is recommended that you create and use a Github PAT. Once you have the PAT, run the following:



```R

Sys.setenv(GITHUB_PAT = "your_access_token_here")

```



Running the `restore_and_run("APP_NAME")` will run the `APP_NAME` by restoring the packages using [renv](https://rstudio.github.io/renv/)



```R

source("https://raw.github.com/insightsengineering/teal.gallery/main/_internal/utils/sourceme.R")



# Run the basic-teal app

restore_and_run("basic-teal")

```



## Development



All `teal` sample apps are wrapped into this repository into it's own sub-directory. All development standards and practices that we currently use for teal app development also apply to this repository.



### Auto-deployment



All the sample apps are automatically deployed every day using the CI in two channels:



- `stable` channel: The code for the Teal apps is taken from the `main` branch of `teal.gallery`, and the NEST packages are installed from the `main` branch of GitHub. This is done using the `deploy_stable.yaml`.

- `dev` channel: The code for the Teal apps is taken from the `dev` branch of `teal.gallery` and the NEST packages are installed from the last `release tag` of GitHub. This is done using the `deploy_dev.yaml`.



_IMPORTANT_: Although we can now test the unreleased features of the NEST packages in deployments, currently, the divergent `dev` and `main` branches must be managed and merged manually as needed to ensure that the apps work fine in both deployment channels, i.e., making sure to merge the app changes from `dev` to `main` by creating a PR.



### Adding a sample app to `teal.gallery`



Adding a sample app involves the following steps:



#### Hard requirements



1. Copy each sample app into a file named `app.R` into a sensible folder name inside it's own directory. The directory has to be named with the `APP_NAME`.

2. Update the `_internal/quarto/demo-apps.yml` with a new `app/title`. This should be the `APP_NAME`.

3. Run the `_internal/utils/generate_app_readme.R` to generate the readme for the app inside it's own directory.



#### Optional/Soft requirements



1. You can snapshot the teal app dependencies using `{renv}` but make sure to snapshot using GitHub references to the teal packages.

2. Create a GIF recording ([KAP](https://getkap.co/) is a good tool for this). Make sure that the dimensions of the GIF is 970x555 px and the size is about 1 MB. (It can be done by recording using KAP in 1470x840 px and rendering 5fps and downsizing 33%). Place the GIF inside the `_internal/quarto/assets/img` directory. Also, make sure that the name of the GIF is `APP_NAME.gif`. Also, make sure to place a static image with the name dimention called `APP_NAME.png` that will be displayed in the demo page when the card is not hovered.

3. Add front-end tests with the help of cypress. Copy the contents of the `js` directory within some other app's directory inside your app directory to get the node dependencies. Place the cypress tests inside the `tests/cypress` inside your app's directory. Please refer to an existing app's tests so that the `.github/deploy.yaml` will automaticall run the cypress tests.