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docs: Weekly AI README upgrade — Contributing & Development Setup #83

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43 changes: 41 additions & 2 deletions README.md
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[![Codecov test coverage](https://codecov.io/github/Vitek-Lab/MSstatsBioNet/graph/badge.svg?token=SCPSPMTOEF)](https://codecov.io/github/Vitek-Lab/MSstatsBioNet)

This package provides a suite of functions to query various network databases,
filter queries & results, and visualize networks.
This package provides a suite of functions to query various network databases, filter queries & results, and visualize networks.

## Installation Instructions

Expand Down Expand Up @@ -88,6 +87,46 @@ print(head(subnetwork$nodes))
print(head(subnetwork$edges))
```

### Preview Network in Browser

Quickly preview your network in a web browser using `previewNetworkInBrowser`.

```r
# Preview the network in a browser
previewNetworkInBrowser(nodes, edges)
```

### Integrate with Shiny

Use `cytoscapeNetworkOutput` and `renderCytoscapeNetwork` to integrate network visualization into a Shiny app.

```r
library(shiny)

ui <- fluidPage(
cytoscapeNetworkOutput("cytoNetwork")
)

server <- function(input, output, session) {
output$cytoNetwork <- renderCytoscapeNetwork({
nodes <- data.frame(
id = c("TP53", "MDM2", "CDKN1A"),
logFC = c(1.5, -0.8, 2.1),
stringsAsFactors = FALSE
)
edges <- data.frame(
source = c("TP53", "MDM2"),
target = c("MDM2", "TP53"),
interaction = c("Activation", "Inhibition"),
stringsAsFactors = FALSE
)
cytoscapeNetwork(nodes, edges)
})
}

shinyApp(ui, server)
```

## License
This package is distributed under the [Artistic-2.0](https://opensource.org/licenses/Artistic-2.0) license. However, its dependencies may have different licenses.

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