plotTopSigGenes: Plot top significantly differentially expressed genes by...

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Plot top significantly differentially expressed genes by contrast

Description

Plot top significantly differentially expressed genes by contrast

Usage

plotTopSigGenes(
  countDgeResult,
  n = 5,
  nSigned = NULL,
  identifier = "GeneSymbol"
)

Arguments

countDgeResult	A CountDgeResult object, for instance EdgeResult or LimmaVoomDgeResult.
n	Integer, how many genes should be visualized per contrast.
nSigned	NULL or integer, in the later case the top nSigned genes from positively and negatively regulated genes are shown per contrast, respectively.
identifier	Character string, column name in genes annotation to be used to index and display the genes.

Value

A ggplot object

See Also

plotTopSigGenesByContrast plots one contrast at a time.

Examples

edgeObj <- exampleEdgeObject()
edgeRes <- dgeWithEdgeR(edgeObj)
plotTopSigGenes(edgeRes, n=6)
## display top two positive and top three negative genes
plotTopSigGenes(edgeRes, nSigned=2)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.