TCGAvisualize_EAbarplot {TCGAbiolinks} | R Documentation

## barPlot for a complete Enrichment Analysis

### Description

The figure shows canonical pathways significantly overrepresented (enriched) by the DEGs (differentially expressed genes). The most statistically significant canonical pathways identified in DEGs list are listed according to their p value corrected FDR (-Log) (colored bars) and the ratio of list genes found in each pathway over the total number of genes in that pathway (Ratio, red line).

### Usage

    TCGAvisualize_EAbarplot(tf, GOMFTab, GOBPTab, GOCCTab, PathTab, nBar,
      nRGTab, filename = "TCGAvisualize_EAbarplot_Output.pdf",
      text.size = 1, mfrow = c(2, 2), xlim = NULL, color = c("orange",
      "cyan", "green", "yellow"))

### Arguments

`tf` | is a list of gene symbols
`GOMFTab` | is results from TCGAanalyze_EAcomplete related to Molecular Function (MF)
`GOBPTab` | is results from TCGAanalyze_EAcomplete related to Biological Process (BP)
`GOCCTab` | is results from TCGAanalyze_EAcomplete related to Cellular Component (CC)
`PathTab` | is results from TCGAanalyze_EAcomplete related to Pathways EA
`nBar` | is the number of bar histogram selected to show (default = 10)
`nRGTab` | is the gene signature list with gene symbols.
`filename` | Name for the pdf. If null it will return the plot.
`text.size` | Text size
`mfrow` | Vector with number of rows/columns of the plot. Default 2 rows/2 columns "c(2,2)"
`xlim` | Upper limit of the x-axis.
`color` | A vector of colors for each barplot. Deafult: c("orange", "cyan","green","yellow")

### Value

Complete barPlot from Enrichment Analysis showing significant (default FDR < 0.01) BP,CC,MF and pathways enriched by list of genes.

### Examples

    Genelist <- c("FN1","COL1A1")
    ansEA <- TCGAanalyze_EAcomplete(TFname="DEA genes Normal Vs Tumor",Genelist)
    TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP),
             GOBPTab = ansEA$ResBP,
             GOCCTab = ansEA$ResCC,
             GOMFTab = ansEA$ResMF,
            PathTab = ansEA$ResPat,
             nRGTab = Genelist,
             nBar = 10,
             filename="a.pdf")
    while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}
    ## Not run:
    Genelist <- rownames(dataDEGsFiltLevel)
    system.time(ansEA <- TCGAanalyze_EAcomplete(TFname="DEA genes Normal Vs Tumor",Genelist))
    # Enrichment Analysis EA (TCGAVisualize)
    # Gene Ontology (GO) and Pathway enrichment barPlot
    TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP),
             GOBPTab = ansEA$ResBP,
             GOCCTab = ansEA$ResCC,
             GOMFTab = ansEA$ResMF,
            PathTab = ansEA$ResPat,
             nRGTab = Genelist,
             nBar = 10)

    ## End(Not run)

[Package TCGAbiolinks version 2.10.5 Index]