MARVEL (version 1.4.0)

PlotDEValues.SJ.10x: Plot differential splice junction analysis results

Description

Volcano plot of results from differential splice junction analysis. x-axis represents the average normalised gene expression across the two cell groups. y-axis represents the differences or log2 fold change between the two cell groups.

Usage

PlotDEValues.SJ.10x(
  MarvelObject,
  pval = 0.05,
  log2fc = NULL,
  delta = 5,
  min.gene.norm = 0,
  anno = FALSE,
  anno.coord.intron = NULL,
  label.size = 2
)

Value

An object of class S3 with a new slots MarvelObject$DE$SJ$VolcanoPlot$SJ$Plot and MarvelObject$DE$SJ$VolcanoPlot$SJ$Data.

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues.Genes.10x function.

pval

Numeric value. p-value, below which, the splice junction is considered differentially spliced. To be used in conjunction with log2fc, delta, and min.gene.norm. Default is 0.05.

log2fc

Numeric value. Absolute log2 fold change, above which, the splice junction is considered differentially spliced. This option should be NULL if delta has been specified.

delta

Numeric value. Absolute differences in average PSI values between the two cell groups, above which, the splice junction is considered differentially spliced. This option should be NULL if log2fc has been specified.

min.gene.norm

Numeric value. The average normalised gene expression across the two cell groups above which the splice junction is considered differentially spliced. Default is 0.

anno

Logical value. If set to TRUE, user-specific spliced genes in anno.coord.intron will be annotated on the plot. Default is FALSE.

anno.coord.intron

Vector of character strings. If anno set to TRUE, splice junction coordinates specified here will be annotated on the plot.

label.size

Numeric value. If anno set to TRUE, the font size of the annotations on the plot will be adjusted to the size specified here. Default is 2.

Examples

marvel.demo.10x <- readRDS(system.file("extdata/data",
                               "marvel.demo.10x.rds",
                               package="MARVEL")
                               )

marvel.demo.10x <- PlotDEValues.SJ.10x(
                        MarvelObject=marvel.demo.10x,
                        pval=0.05,
                        delta=5,
                        min.gene.norm=1.0,
                        anno=FALSE
                        )

# Check outputs
marvel.demo.10x$DE$SJ$VolcanoPlot$SJ$Plot
head(marvel.demo.10x$DE$SJ$VolcanoPlot$SJ$Data)