pathVar (version 1.2.0)

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

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.

Value

A pdf of the results from sigPway.

Details

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

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")

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