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.

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.

# 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.

# 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.

# 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.

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

Integrate with Shiny

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

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 license. However, its dependencies may have different licenses.

Notably, INDRA is distributed under the BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may have different licenses for commercial applications. Please refer to the INDRA README 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