plot_ppi_enrichment_graph {STRINGdb} | R Documentation |
Plots a graph showing the enrichment in protein interactions in various positions of the list of genes in input.
plot_ppi_enrichment_graph(proteins, ppi_network, file, sliceWindow, edgeWindow, windowExtendedReferenceThreshold, minVal, title, quiet)
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) |
Andrea Franceschini
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)