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

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

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
)

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.

Value

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

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)

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