plot,pePathway,missing-method {ROntoTools} | R Documentation

## 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

    ## 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")

[Package ROntoTools version 2.10.0 Index]