tna.plot.gsea2: Plot enrichment analyses from TNA objects.

In RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Description

This function takes a TNA object and plots the two-tailed GSEA results for individual regulons.

Usage

tna.plot.gsea2(object, labPheno="", file="tna_gsea2", filepath=".", 
regulon.order="size", ntop=NULL, tfs=NULL, ylimPanels=c(-3.0,3.0,-0.5,0.5), 
heightPanels=c(2.0,0.8,5.0), width=2.8, height=3.0, 
ylabPanels=c("Phenotype","Regulon","Enrichment score"), 
xlab="Position in the ranked list of genes", alpha=1.0, 
sparsity=10, autoformat=TRUE, plotpdf=TRUE, ...)

Arguments

object	an object of class 'TNA' TNA-class.
file	a character string naming a file.
filepath	a single character value specifying where to store GSEA2 figures.
regulon.order	a single character value specifying whether regulons should be ordered by 'size', 'score', 'pvalue', 'adj.pvalue' and 'name' (or 'none' to keep the input ordering).
ntop	a single integer value specifying how many regulons of top significance will be plotted.
tfs	an optional vector with transcription factor identifiers (this option overrides the 'ntop' argument).
ylimPanels	a numeric vector of length=4 specifying y coordinates ranges of the 1st and 3th plots (i.e. ylim for 'Phenotypes' and 'Running enrichment score').
heightPanels	a numeric vector of length=3 specifying the relative height of each panel in the plot.
width	a single numeric value specifying the width of the graphics region in inches.
height	a single numeric value specifying the height of the graphics region in inches.
ylabPanels	a character vector of length=3 specifying the the title for the y axes.
xlab	a single character specifying the the title for the x axis.
labPheno	a single character specifying a label for the phenotype (will also be used as the name of output file).
alpha	a single numeric value in [0,1] specifying the transparency of the hits in the ranked list.
sparsity	a single integer value (>1) specifying the density of the dots representing the running score.
autoformat	a single logical value specifying to set the graph format using predefined themes. This option overrides the "ylimPanels" argument.
plotpdf	a single logical value specifying to whether to plot a PDF file or directly to Viewer.
...	other arguments used by the function pdf.

Value

A plot showing results from the 'tna.gsea2' method.

Author(s)

Mauro Castro

See Also

tna.gsea2

Examples

data(tniData)
data(tnaData)

## Not run: 

rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)
rtni <- tni.permutation(rtni)
rtni <- tni.bootstrap(rtni)
rtni <- tni.dpi.filter(rtni)
rtna <- tni2tna.preprocess(rtni, phenotype=tnaData$phenotype, 
        hits=tnaData$hits, phenoIDs=tnaData$phenoIDs)

# run GSEA2 analysis pipeline
rtna <- tna.gsea2(rtna)

# plot available GSEA2 results
tna.plot.gsea2(rtna, labPheno="test")

## End(Not run)

RTN documentation built on Nov. 12, 2020, 2:02 a.m.