plot,pePathway,missing-method {ROntoTools} | R Documentation |
Display graphical representation of pathway level statistic like:
i) two way comparison between the measured expression change and one of the
factors computed by Pathway-Express (pe
) or ii) the boostrap
statistics of the same factors.
## S4 method for signature 'pePathway,missing' plot(x, y, ..., type = "two.way", eps = 1e-06) ## S4 method for signature 'pePathway,character' plot(x, y, main = "", ..., type = "two.way", eps = 1e-06)
x |
an object of type |
y |
if provided, the factor to be ploted (either |
... |
Arguments to be passed to methods, such as |
type |
type of plot (either |
eps |
any value smaller than this will be ploted as 0 |
main |
title |
Calin Voichita and Sorin Draghici
pe
, plot,peRes,missing-method
, peNodeRenderInfo
, peEdgeRenderInfo
# load experiment load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools")) fc <- top$logFC[top$adj.P.Val <= .01] names(fc) <- top$entrez[top$adj.P.Val <= .01] ref <- top$entrez # load the set of pathways kpg <- keggPathwayGraphs("hsa") kpg <- setEdgeWeights(kpg) kpg <- setNodeWeights(kpg, defaultWeight = 1) # perform the pathway analysis (for more accurate results use nboot = 2000) peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE) plot(peRes@pathways[[50]]) plot(peRes@pathways[[50]], "Pert", main = "Perturbation factor") plot(peRes@pathways[[50]], type = "boot") plot(peRes@pathways[[50]], "Pert", type = "boot", main = "Perturbation factor")