GSEA.barplot: Visualize the gene set enrichment analysis

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/GSEA.barplot.R

Description

For the functional enrichment analysis, we can visualize the result from the gene set enrichment analysis.

Usage

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GSEA.barplot(object, category, score, pvalue, top = 10,
             sort = NULL, decreasing = FALSE, numChar = NULL, 
             title = NULL, transparency = 0.5, plot = TRUE)

Arguments

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)

Value

GSEA barplot

Author(s)

Dongmin Jung, Xijin Ge

References

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.

See Also

ggplot2

Examples

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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) +
             scale_fill_continuous(low = 'red', high = 'green')

PPInfer documentation built on Nov. 1, 2018, 2:10 a.m.