networkView: Visualization of the interactions between input proteins

Description Usage Arguments Details Value References See Also Examples

Description

This method can visualize the input proteins in the protein–protein interaction (PPI) network and display the evidence that supports the specific interactions among these proteins.

Usage

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networkView(infoFile, proteinNames, outputDir, swissProtID=FALSE, mainNode=c(1), nodeColors=c("#1F77B4", "#FF7F0E", "#D62728","#9467BD","#8C564B","#E377C2"), displayMore=TRUE, leafColor="#2CA02C")
## S4 method for signature 'character,character,character'
networkView(infoFile, proteinNames, outputDir, swissProtID=FALSE, mainNode=c(1), nodeColors=c("#1F77B4", "#FF7F0E", "#D62728","#9467BD","#8C564B","#E377C2"), displayMore=TRUE, leafColor="#2CA02C")

Arguments

infoFile

File that contains PPI data (character(1)).
Please see the file PPI_Info.txt as an example.

proteinNames

Gene names or Swiss-Prot accession numbers of the proteins (character vector).

outputDir

Output directory (character(1)).

swissProtID

A logical value. If proteinNames contains Swiss-Prot accession numbers, set as TRUE.
If proteinNames contains gene names, set as FALSE.

mainNode

A vector of value 0 and 1.
0: display the corresponding protein as a leaf node.
1: display the corresponding protein as a main node.
If there are fewer values than proteins, it will be recycled in the standard manner.

nodeColors

Represents colors for proteins. If there are fewer values than proteins, it will be recycled in the standard manner.
Form: "#RRGGBB", each of the pairs RR, GG, BB consist of two hexadecimal digits giving a value in the range 00 to FF.

displayMore

A logical value. If TRUE, other proteins will be displayed which can interact with at least two proteins in proteinNames.

leafColor

Only used while displayMore=TRUE. This is the color for additional proteins. (character(1))
Form: "#RRGGBB", each of the pairs RR, GG, BB consist of two hexadecimal digits giving a value in the range 00 to FF.

Details

As an example, we have generated PPI interaction data for several species from the PINA database (http://cbg.garvan.unsw.edu.au/pina/) and the STRING database (http://string-db.org/). Users can download these files from http://www.isb.pku.edu.cn/cisPath/. If you make use of these files, please cite PINA or STRING accordingly. Users can edit the PPIs generated with these two databases, or combine them with their private data to construct more complete PPI networks. In this package, we select only a small portion of the available PPI data as an example.

A protein often has several names, and some of these names have perhaps not been included in the input file infoFile. We therefore suggest users take a look at the output file proteinIDs.txt to check whether the input protein names are valid. In order to avoid inputting invalid target protein names, the unique identifier Swiss-Prot accession numbers may alternatively be used as input. The Swiss-Prot accession numbers can be sought in the UniProt (http://www.uniprot.org/) database.

Value

The output HTML file contains the PPIs and related evidence supporting them. Users can view the PPI network and the evidence supporting these interactions easily using a browser. Please take a look at the output file proteinIDs.txt to check whether the input protein names are valid.

References

Cowley, M.J. and et al. (2012) PINA v2.0: mining interactome modules. Nucleic Acids Res, 40, D862-865.

Wu, J. and et al. (2009) Integrated network analysis platform for protein-protein interactions. Nature methods, 6, 75-77.

Szklarczyk,D. and et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res, 39, D561-D568.

Franceschini,A. and et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res, 41, D808-D815.

UniProt Consortium and others. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40, D71-D75.

See Also

cisPath, easyEditor.

Examples

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    library(cisPath)
    infoFile <- system.file("extdata", "PPI_Info.txt", package="cisPath")
    outputDir <- file.path(tempdir(), "networkView")
    networkView(infoFile, c("MAGI1","TP53BP2","TP53", "PTEN"), outputDir, FALSE, c(1,1,1,0), displayMore=TRUE)
    
    outputDir2 <- file.path(tempdir(), "networkView2")
    inputFile <- system.file("extdata", "networkView.txt", package="cisPath")
    rt <- read.table(inputFile, sep=",", comment.char="", header=TRUE)
    proteins <- as.vector(rt[,1])
    sizes <- as.vector(rt[,2])
    nodeColors <- as.vector(rt[,3])
    networkView(infoFile, proteins, outputDir2, FALSE, sizes, nodeColors, displayMore=FALSE)

cisPath documentation built on Nov. 17, 2017, 10:36 a.m.