TCGAbiolinks (version 1.2.5)

TCGAvisualize_EAbarplot: 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)