plot_ppi_enrichment_graph {STRINGdb} | R Documentation

## plot_ppi_enrichment_graph

### Description

Plots a graph showing the enrichment in protein interactions in various positions of the list of genes in input.

### Usage

    plot_ppi_enrichment_graph(proteins, ppi_network, file, sliceWindow, edgeWindow, windowExtendedReferenceThreshold, minVal, title, quiet)

### Arguments

`proteins` | a vector of protein identifiers
`ppi_network` | an igraph object containing the protein-protein interactions' graph.
`file` | file where to save the graph as an image
`sliceWindow` | defines the interval in proteins after which to compute the enrichment, scanning the list (i.e. the resolution)
`edgeWindow` | size of the window that we use to compute the enrichment (i.e. the window pvalue is computed using the proteins inside this "edgeWindow")
`windowExtendedReferenceThreshold` | defines the size of a window at the beginning of the list. The enrichment will be computed always including the proteins in this window
`title` | title of the graph.
`minVal` | minimum value that the pvalue can assume in the log-scale graph. If the p-value is lower, we convert the value to this minimum value
`quiet` | if set to TRUE the method runs in quiet mode (turning off any output message)

### Author(s)

Andrea Franceschini

### References

Pradines JR, Farutin V, Rowley S, Dancik V. Analyzing protein lists with large networks: edge-count probabilities in random graphs with given expected degrees. J. Comput. Biol. 2005;12:113-128. Franceschini, A et al. (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. In:Nucleic Acids Res. 2013 Jan;41(Database issue)

[Package STRINGdb version 1.26.0 Index]