adhocGene.PlotDEValues.10x: Plot differential splice junction analysis results for a...

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Plot differential splice junction analysis results for a specified gene

Description

Scatterplot of results from differential gene and splice junction analysis. x-axis represents the gene expression log2 fold change between the different pairs of cell groups. y-axis represents the PSI differences or log2 fold change between the different pairs of cell groups.

Usage

adhocGene.PlotDEValues.10x(
  MarvelObject,
  coord.intron,
  log2fc.gene = 0.5,
  delta.sj = 5,
  label.size = 2,
  point.size = 2,
  xmin = NULL,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL
)

Arguments

MarvelObject	Marvel object. S3 object generated from adhocGene.DE.Gene.10x and adhocGene.DE.PSI.10x functions.
coord.intron	Character string. Coordinates of splice junction whose differential splice junction results will be plotted.
log2fc.gene	Numeric value. Absolute log2 fold change, above which, the gene is considered differentially expressed.
delta.sj	Numeric value. Absolute differences in average PSI values between the two cell groups, above which, the splice junction is considered differentially spliced.
label.size	Numeric value. The font size of the group comparison labels on the plot will be adjusted to the size specified here. Default is 2.
point.size	Numeric value. Size of data points. Default is 2.
xmin	Numeric value. Minimum x-axis value.
xmax	Numeric value. Maximum x-axis value.
ymin	Numeric value. Minimum y-axis value.
ymax	Numeric value. Maximum y-axis value.

Value

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

Examples

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

# Define SJ to plot
coord.intron <- marvel.demo.10x$adhocGene$DE$PSI$Data$coord.intron[1]

# Plot SJ vs gene
marvel.demo.10x <- adhocGene.PlotDEValues.10x(
                        MarvelObject=marvel.demo.10x,
                        coord.intron=coord.intron,
                        log2fc.gene=0.5,
                        delta.sj=5,
                        label.size=2,
                        point.size=2,
                        xmin=-2.0,
                        xmax=2.0,
                        ymin=-25,
                        ymax=25
                        )

# Check output
marvel.demo.10x$adhocGene$DE$VolcanoPlot$Plot

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