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)