PlotDEValues.Exp.Global {MARVEL}

Plot global differential gene expression analysis results

Description

Volcano plot of differential splicing analysis results based on all expressed 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.Global(
  MarvelObject,
  pval = 0.1,
  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

Marvel object. S3 object generated from CompareValues function.

pval

Numeric value. Adjusted p-value below which the genes are considered as statistically significant and will consequently be color-annotated on the plot.

log2fc

Numeric value. The positive (and negative) value specified above (and below) which the genes are considered to be statistically significant and will consequently be color-annotated on the plot.

point.size

Numeric value. The point size for the data points. Default value 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.Global$Table, MarvelObject$DE$Exp.Global$Summary, and MarvelObject$DE$Exp.Global$Plot

Examples

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

marvel.demo <- PlotDEValues.Exp.Global(MarvelObject=marvel.demo,
                                       pval=0.10,
                                       log2fc=0.5
                                       )

# Check output
head(marvel.demo$DE$Exp.Global$Table)
marvel.demo$DE$Exp.Global$Plot
marvel.demo$DE$Exp.Global$Summary