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, ...)

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.

...

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
data(dt4rtn)

tfs4test<-c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")
rtni <- new("TNI", gexp=dt4rtn$gexp, transcriptionFactors=dt4rtn$tfs[tfs4test])

## Not run: 

rtni <- tni.preprocess(rtni,gexpIDs=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 May 20, 2017, 10:08 p.m.
Search within the RTN package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.