Last data update: 2014.03.03

R: Checks if an object is from the one sample or two samples...
plotPwayR Documentation

Checks if an object is from the one sample or two samples cases and then plots reference distribution and the chosen pathway.

Description

Checks if an object is from the one sample or two samples cases and then plots reference distribution and the chosen pathway.

Usage

plotPway(pvalue_results,pathway,sig)

Arguments

pvalue_results

output of pathVarTwoSamples or pathVarOneSample step.

pathway

the chosen pathway you want to plot.

sig

output of sigPway or NULL.

Details

Plots the results of the one or two samples case for a chosen pathway.

Value

A plot of the results from sigPway.

Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Examples

# we run the 2 samples analysis on the first 10 pathways from kegg
pways.kegg.10pways <- lapply(pways.kegg, function(x) x[1:10])
results_2samples=pathVarTwoSamplesCont(bock,pways.kegg.10pways,groups=as.factor(c(rep(1,10),rep(2,10))))
sigPways <- sigPway(results_2samples,0.05)
plotPway(results_2samples,"Glycolysis / Gluconeogenesis",sigPways)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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(pathVar)
Loading required package: ggplot2
Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pathVar/plotPway.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPway
> ### Title: Checks if an object is from the one sample or two samples cases
> ###   and then plots reference distribution and the chosen pathway.
> ### Aliases: plotPway
> ### Keywords: methods
> 
> ### ** Examples
> 
> # we run the 2 samples analysis on the first 10 pathways from kegg
> pways.kegg.10pways <- lapply(pways.kegg, function(x) x[1:10])
> results_2samples=pathVarTwoSamplesCont(bock,pways.kegg.10pways,groups=as.factor(c(rep(1,10),rep(2,10))))
> sigPways <- sigPway(results_2samples,0.05)
> plotPway(results_2samples,"Glycolysis / Gluconeogenesis",sigPways)
Using X1, X2 as id variables
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>