tna.plot.gsea1: Plot enrichment analyses from TNA objects.

Description Usage Arguments Author(s) See Also Examples

View source: R/AllPlotsTNA.R

Description

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

Usage

1
2
3
4
5
tna.plot.gsea1(object, labPheno="tna", file=labPheno, filepath=".", regulon.order="size", 
ntop=NULL, tfs=NULL, ylimPanels=c(0.0,3.5,0.0,0.8), heightPanels=c(1,1,3), 
width=4.4, height=4, ylabPanels=c("Phenotype","Regulon","Enrichment score"), 
xlab="Position in the ranked list of genes", alpha=0.5, 
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 GSEA 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 value specifying the the title for the x axis.

labPheno

a single character value 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.

Author(s)

Mauro Castro

See Also

tna.gsea1

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
data(dt4rtn)

# select 5 regulatoryElements for a quick demonstration!
tfs4test <- dt4rtn$tfs[c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")]

## Not run: 

rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test, 
        rowAnnotation=dt4rtn$gexpIDs)
rtni<-tni.permutation(rtni)
rtni<-tni.bootstrap(rtni)
rtni<-tni.dpi.filter(rtni)
rtna<-tni2tna.preprocess(rtni, phenotype=dt4rtn$pheno, hits=dt4rtn$hits, phenoIDs=dt4rtn$phenoIDs)

# run GSEA analysis pipeline
rtna <- tna.gsea1(rtna, stepFilter=FALSE)

# plot available GSEA results
tna.plot.gsea1(rtna, labPheno="test")

## End(Not run)

RTN documentation built on Nov. 17, 2017, 1:44 p.m.