saveAsPDF: Save the plots of the significant pathway or a chosen list of...

In jmarlab/pathVar: Methods to Find Pathways with Significantly Different Variability

Description

Save the plots of the significant pathway or a chosen list of pathways as a pdf.

Usage

saveAsPDF(pvalue_results,sig,listPath="significant")

Arguments

pvalue_results	output of pathVarTwoSamples or pathVarOneSample step.
sig	output of sigPway or NULL.
listPath	the string "significant" if you want to save the plots of the significant pathways or a list of names of pathways of interest.

Details

Save the plots of the significant pathway or a chosen list of pathways as a pdf.

Value

A pdf 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)
saveAsPDF(results_2samples,sigPways,listPath="significant")

jmarlab/pathVar documentation built on May 23, 2019, 9:02 p.m.