plot_ppi_enrichment {STRINGdb} | R Documentation

## plot_ppi_enrichment

### Description

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

### Usage

    ## S4 method for signature 'STRINGdb'
    plot_ppi_enrichment(string_ids, file=NULL, sliceWindow = 20, edgeWindow = 140,
                                         windowExtendedReferenceThreshold = 260, minVal=0.0000000001, title="", quiet=FALSE)

### Arguments

`string_ids` | a vector of STRING identifiers
`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

[Package STRINGdb version 1.22.0 Index]