Last data update: 2014.03.03

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

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

### Examples

```
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")

```

### Results

```
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ROntoTools)

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

The following objects are masked from 'package:base':

Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

plot

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ROntoTools/plot.pePathway-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot,pePathway,missing-method
> ### Title: Plot pathway level statistics
> ### Aliases: plot,pePathway,character-method plot,pePathway,missing-method
>
> ### ** Examples
>
>
> 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")
Using cached pathway data. Database info:
pathway          KEGG Pathway Database
path             Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
> 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)
Performing pathway analysis...
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>
> 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")
>
>
>
>
>
>
> dev.off()
null device
1
>

```