MARVEL (version 1.4.0)

AnnoVolcanoPlot: Annotate volcano plot with nonsense-mediated decay (NMD) genes

Description

Annotate volcano plot generated from differential gene expression analysis with genes predicted to undergo splicing-induced NMD.

Usage

AnnoVolcanoPlot(
  MarvelObject,
  anno = FALSE,
  anno.gene_short_name = NULL,
  label.size = NULL,
  point.size = 1,
  xlabel.size = 8
)

Value

An object of class S3 with new slots MarvelObject$NMD$AnnoVolcanoPlot$Table and MarvelObject$NMD$AnnoVolcanoPlot$Plot.

Arguments

MarvelObject

Marvel object. S3 object generated from CompareExpr function.

anno

Logical value. If set to TRUE, selected gene names will be annotated on the plot as defined in gene.label.x.below and gene.label.y.above.

anno.gene_short_name

Vector of character strings. When anno set to TRUE, the gene names to annotate on the plot.

label.size

Numeric value. When anno set to TRUE, the size of gene labels.

point.size

Numeric value. Size of data points. Default value is 1.

xlabel.size

Numeric value. Font size of the xtick labels. Default is 8.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

marvel.demo <- AnnoVolcanoPlot(MarvelObject=marvel.demo)

# Check outputs
head(marvel.demo$NMD$AnnoVolcanoPlot$Table)
marvel.demo$NMD$AnnoVolcanoPlot$Plot