# MSstatsBioNet
[](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.
## Installation Instructions
To install this package on bioconductor, run the following command:
```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSstatsBioNet")
```
You can install the development version of this package through Github:
```
devtools::install_github("Vitek-Lab/MSstatsBioNet", build_vignettes = TRUE)
```
## Usage Examples
Here are some examples to help you get started with MSstatsBioNet:
### Annotate Protein Information
Use the `annotateProteinInfoFromIndra` function to annotate a data frame with protein information from Indra.
```r
library(MSstatsBioNet)
# Example data frame
df <- data.frame(Protein = c("CLH1_HUMAN"))
# Annotate protein information
annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot_Mnemonic")
print(head(annotated_df))
```
### Visualize Networks with Cytoscape
Create an interactive network diagram using `cytoscapeNetwork`.
```r
# Define nodes and edges
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
)
# Render the network
cytoscapeNetwork(nodes, edges)
```
### Export Network to HTML
Export your network visualization to an HTML file using `exportNetworkToHTML`.
```r
# Export the network to an HTML file
exportNetworkToHTML(nodes, edges, filename = "network.html")
```
### Retrieve Subnetwork from INDRA
Use `getSubnetworkFromIndra` to retrieve a subnetwork of protein interactions from the INDRA database.
```r
# Load example input data
input <- data.table::fread(system.file(
"extdata/groupComparisonModel.csv",
package = "MSstatsBioNet"
))
# Get subnetwork
subnetwork <- getSubnetworkFromIndra(input)
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.
Notably, INDRA is distributed under the [BSD 2-Clause](https://opensource.org/license/bsd-2-clause) license. Furthermore, INDRA's knowledge sources may have different licenses for commercial applications. Please refer to the [INDRA README](https://github.com/sorgerlab/indra?tab=readme-ov-file#indra-modules) for more information on its knowledge sources and their associated licenses.
## Databases Supported
- INDRA
## Filtering Options Supported
- P-Value Filter
## Visualization Options Supported
- Cytoscape Desktop
