TCGAvisualize_EAbarplot: barPlot for a complete Enrichment Analysis

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

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$ResPat,
         nRGTab = Genelist,
         nBar = 10,
         filename="a.pdf")
## Not run: 
Genelist <- rownames(dataDEGsFiltLevel)
system.time(ansEA <- TCGAanalyze_EAcomplete(TFname="DEA genes Normal Vs Tumor",Genelist))
# Enrichment Analysis EA (TCGAVisualize)
# Gene Ontology (GO) and Pathway enrichment barPlot
TCGAvisualize_EAbarplot(tf = rownames(ansEA$ResBP),
         GOBPTab = ansEA$ResBP,
         GOCCTab = ansEA$ResCC,
         GOMFTab = ansEA$ResMF,
        PathTab = ansEA$ResPat,
         nRGTab = Genelist,
         nBar = 10)

## End(Not run)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.