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

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

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
)

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.

Value

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

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

MARVEL documentation built on Oct. 31, 2022, 5:07 p.m.