ROntoTools (version 2.0.0)

plot,pePathway,missing-method: Plot pathway level statistics

Description

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.

Usage

"plot"(x, y, ..., type = "two.way", eps = 1e-06)
"plot"(x, y, main = "", ..., type = "two.way", eps = 1e-06)

Arguments

x

an object of type pePathway-class

y

if provided, the factor to be ploted (either Acc (default) or Pert; see pePathway-class)

...

Arguments to be passed to methods, such as par

type

type of plot (either two.way (default) or boot)

eps

any value smaller than this will be ploted as 0

main

title

See Also

pe, plot,peRes,missing-method, peNodeRenderInfo, peEdgeRenderInfo

Examples

# 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")