plot.pePathway-methods: Plot pathway level statistics

In ROntoTools: R Onto-Tools suite

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

## 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)

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

Author(s)

Calin Voichita and Sorin Draghici

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")

ROntoTools documentation built on Nov. 8, 2020, 7:41 p.m.