feat: revised docs on running locally

README.md

@@ -25,45 +25,71 @@ This app has the following simple goals:
 
 1.   ease quick data overview and basic visualisations for any clinical researcher
 
-## Run locally on your own machine
+Here’s a polished and restructured version of your README section for clarity, conciseness, and user-friendliness:
 
-The ***FreesearchR*** app can also run on your own machine with no data transmitted anywhere. Blow are the available options.
+## Run Locally on Your Own Machine
 
-### Run from R (or RStduio)
+The **FreesearchR** app can be run locally on your machine, ensuring no data is transmitted externally. Below are the available options for setup and configuration.
 
-Working with data in R, FreesearchR is a quick and easy tool to get overview and perform the first explorative analyses to get you going.
+### Configuration & Data Loading
 
-Any data available in the your R session will be available to the FreesearchR app. Just follow the below steps to get going:
+The app can be configured either by passing a named list to `run_app()` or by setting environment variables in a **Docker Compose** file. The following variables control data access and display behavior. If no values are provided, the app will use the defaults listed below.
 
-1.   **Requirement:** You need to have [*R* installed](https://www.r-project.org/) and possibly an editor like [RStudio](https://posit.co/download/rstudio-desktop/). 
 
-1.   Then open the *R* console and copy/paste the following code, that will install the `{devtools}` package and then the `{FreesearchR}` *R*-package with its dependencies:
+**Configuration Variables**
 
-     ```
-     require("devtools")
+| Variable                | Description                                                                 | Default   |
+|-------------------------|-----------------------------------------------------------------------------|-----------|
+| `INCLUDE_GLOBALENV`     | Load datasets already present in the global R environment into the app    | `FALSE`   |
+| `DATA_LIMIT_DEFAULT`    | Default number of observations for previewing or working with a dataset            | `10,000`  |
+| `DATA_LIMIT_UPPER`      | Maximum number of observations a user can set for the upper limit                    | `100,000` |
+| `DATA_LIMIT_LOWER`      | Minimum number of observations a user can set for the lower limit                    | `1`       |
+
+### Run from R (or RStudio)
+
+If you're working with data in R, **FreesearchR** is a quick and easy tool for exploratory analysis.
+
+1. **Requirement:** Ensure you have [R](https://www.r-project.org/) installed, and optionally an editor like [RStudio](https://posit.co/download/rstudio-desktop/).
+
+2. Open the **R console** and run the following code to install the `{FreesearchR}` package and launch the app:
+
+   ```r
+   if (!require("devtools")) install.packages("devtools")
    devtools::install_github("agdamsbo/FreesearchR")
    library(FreesearchR)
-     # By loading mtcars to the environment, it will be available 
-     # in the interface like any other data.frame
+   # Load sample data (e.g., mtcars) to make it available in the app
    data(mtcars)
-     launch_FreesearchR()
+   launch_FreesearchR(INCLUDE_GLOBALENV=TRUE)
    ```
 
-### Running with docker compose
+All the variables specified above can also be passed to the app on launch from R.
 
-For advanced users, wanting to deploy the FreesearchR app to run anywhere, a docker image is available.
+### Running with Docker Compose
 
-Below is the minimal `docker_compose.yml` file:
+For advanced users, you can deploy **FreesearchR** using Docker. A data folder can be mounted to `/app/data` to automatically load supported file types (`.csv`, `.tsv`, `.txt`, `.xls`, `.xlsx`, `.ods`, `.dta`, `.rds`) at startup.
 
-```
+To mount a local data folder, add a `volumes` entry to your `docker-compose.yml` file:
+
+```yaml
 services:
-  freesearchr: 
+  shiny:
     image: ghcr.io/agdamsbo/freesearchr:latest
+    volumes:
+      - ./data:/app/data:ro
+    environment:
+      - INCLUDE_GLOBALENV=FALSE
+      - DATA_LIMIT_DEFAULT=10000
+      - DATA_LIMIT_UPPER=100000
+      - DATA_LIMIT_LOWER=1
     ports:
       - '3838:3838'
     restart: on-failure
 ```
 
+- The `:ro` flag mounts the folder as **read-only**, preventing the app from modifying your original data files.
+
+- If no volume is mounted, the app will start without any preloaded datasets.
+
 ## Code of Conduct
 
 Please note that the ***FreesearchR*** project is published with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.