plot_ppi_enrichment {STRINGdb} | R Documentation |
Plots a graph showing the enrichment in protein interactions in various positions of the list of genes in input.
## S4 method for signature 'STRINGdb' plot_ppi_enrichment(string_ids, file=NULL, sliceWindow = 20, edgeWindow = 140, windowExtendedReferenceThreshold = 260, minVal=0.0000000001, title="", quiet=FALSE)
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) |
Andrea Franceschini