TCGAvisualize_EAbarplot {TCGAbiolinks} | R Documentation |
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).
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"))
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") |
Complete barPlot from Enrichment Analysis showing significant (default FDR < 0.01) BP,CC,MF and pathways enriched by list of genes.
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)