tna.plot.gsea2 {RTN} | R Documentation

## Plot enrichment analyses from TNA objects.

### Description

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

### Usage

    tna.plot.gsea2(object, labPheno="tna", file=labPheno, 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.

### Author(s)

Mauro Castro

### See Also

`tna.gsea2`

### Examples

    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 GSEA2 analysis pipeline
    rtna <- tna.gsea2(rtna, stepFilter=FALSE)

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

    ## End(Not run)

[Package RTN version 2.6.3 Index]