PlotDEValues.Exp.Spliced {MARVEL}

Plot differential gene expression analysis of differentially spliced genes

Description

Volcano plot of differential splicing analysis results based on differentially spliced genes between 2 groups of cells. x-axis represents the log2 fold change in gene expression. y-axis represents the adjusted p-values.

Usage

PlotDEValues.Exp.Spliced(
  MarvelObject,
  method,
  psi.pval = 0.1,
  psi.delta = 0,
  gene.pval = 0.1,
  gene.log2fc = 0.5,
  point.size = 1,
  anno = FALSE,
  anno.gene_short_name = NULL,
  label.size = 2.5,
  y.upper.offset = 5,
  xlabel.size = 8
)

Arguments

MarvelObject

S3 object generated from CompareValues function.

method

(Vector of) Character string(s). The method specified in CompareValues function when level option set to "splicing".

psi.pval

Numeric value. The adjusted p-value from differential splicing analysis, below which, the splicing event is considered differentially spliced. Default is 0.1.

psi.delta

Numeric value. The absolute differences in average PSI value between two cell groups from differential splicing analysis, above which, the splicing event is considered differentially spliced. Default is 0.

gene.pval

Numeric value. The adjusted p-value from differential gene expression analysis, below which, the gene is considered differentially expressed. Default is 0.1.

gene.log2fc

Numeric value. The absolute log2 fold change in gene expression betwene two cell groups from differential splicing analysis, above which, the gene is considered differentially expressed. Default is 0.5.

point.size

Numeric value. Size of data points. Default is 1.

anno

Logical value. If set to TRUE, the specific gene names will be annotated on the plot as defined in anno.gene_short_name option.

anno.gene_short_name

Vector of character strings. When anno set to TRUE, the gene names to be annotated on the plot.

label.size

Numeric value. Only applicable if anno set to TRUE. Size of the gene name labels.

y.upper.offset

Numeric value. The value in -log10(p-value) to increase the upper limit of the y-axis. To be used when anno set to TRUE so that gene labels will not be truncated at the upper limit of the y-axis.

xlabel.size

Numeric value. Font size of the xtick labels. Default is 8.

Value

An object of class S3 with new slots MarvelObject$DE$Exp.Spliced$Table, MarvelObject$DE$Exp.Spliced$Summary, and MarvelObject$DE$Exp.Spliced$Plot.

Examples

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

marvel.demo <- PlotDEValues.Exp.Spliced(MarvelObject=marvel.demo,
                                        method="ad",
                                        psi.pval=0.1,
                                        psi.delta=0,
                                        gene.pval=0.1,
                                        gene.log2fc=0.5
                                        )
# Check output
marvel.demo$DE$Exp.Spliced$Summary
marvel.demo$DE$Exp.Spliced$Plot