PlotDEValues.Exp.Global {MARVEL} | R Documentation |
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 |
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 |
anno |
Logical value. If set to |
anno.gene_short_name |
Vector of character strings. When |
label.size |
Numeric value. Only applicable if |
y.upper.offset |
Numeric value. The value in -log10(p-value) to increase the upper limit of the y-axis. To be used when |
xlabel.size |
Numeric value. Font size of the xtick labels. Default is |
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