GSEA.barplot {PPInfer} | R Documentation |
For the functional enrichment analysis, we can visualize the result from the gene set enrichment analysis.
GSEA.barplot(object, category, score, pvalue, top = 10, sort = NULL, decreasing = FALSE, numChar = NULL, title = NULL, transparency = 0.5, plot = TRUE)
object |
a table with category, enrichment score and p-value of gene sets |
category |
name of gene sets |
score |
enrichment score |
pvalue |
p-value of gene sets |
top |
the number of top categories (default: 10) |
sort |
a variable used for sorting data |
decreasing |
logical indicating whether ascending or descending order (default: FALSE) |
numChar |
the maximal number of characters of the name of gene sets |
title |
title for the plot |
transparency |
transparency (default: 0.5) |
plot |
return plot when plot is true, otherwise return table (default: TRUE) |
GSEA barplot
Dongmin Jung, Xijin Ge
Yu G, Wang L, Yan G and He Q (2015). "DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis." Bioinformatics, 31(4), pp. 608-609.
ggplot2
data(examplePathways) data(exampleRanks) set.seed(1) result.GSEA <- fgsea(examplePathways, exampleRanks, nperm = 1000) GSEA.barplot(result.GSEA, category = 'pathway', score = 'NES', pvalue = 'pval', sort = 'NES', decreasing = TRUE)