MARVEL (version 1.4.0)

PlotDEValues.Genes.10x: Plot differential gene analysis results

Description

Volcano plot of results from differential gene expression analysis. x-axis represents the log2 fold change between two cell groups. y-axis represents -log10(adjusted p-value). Only genes whose splice junctions were considered to be differentially spliced are included for plotting.

Usage

PlotDEValues.Genes.10x(
  MarvelObject,
  pval.sj = 0.05,
  log2fc.sj = NULL,
  delta.sj = 5,
  min.gene.norm = 0,
  pval.adj.gene = 0.05,
  log2fc.gene = 0.5,
  anno = FALSE,
  anno.gene_short_name = NULL,
  label.size = 2
)

Value

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

Arguments

MarvelObject

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

pval.sj

Numeric value. p-value from differential splicing analysis, below which, the splice junction is considered differentially spliced. Default is 0.05.

log2fc.sj

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

delta.sj

Numeric value. Absolute difference 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.sj 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.

pval.adj.gene

Numeric value. Adjusted p-value from differential gene expression analysis, below which, the gene is considered differentially expressed. Default is 0.05.

log2fc.gene

Numeric value. Absolute log2 fold change from differential gene expression analysis, above which, the gene is considered differentially expressed. This option should be NULL if delta.sj has been specified.

anno

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

anno.gene_short_name

Vector of character strings. If anno set to TRUE, genes 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.Genes.10x(
                        MarvelObject=marvel.demo.10x,
                        pval.sj=0.05,
                        delta.sj=5,
                        min.gene.norm=1.0,
                        pval.adj.gene=0.05,
                        log2fc.gene=0.5
                        )

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