MARVEL (version 1.4.0)

adhocGene.PlotDEValues.10x: 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
)

Value

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

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.

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