PlotDEValues.PSI.Mean: Plot differential splicing analysis results based on mean PSI...

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Plot differential splicing analysis results based on mean PSI difference

Description

Volcano plot of differential splicing analysis results based on mean PSI difference between 2 groups of cells. x-axis represents the mean delta PSI. y-axis represents the adjusted p-values.

Usage

PlotDEValues.PSI.Mean(
  MarvelObject,
  method,
  pval = 0.1,
  delta = 5,
  point.size = 1,
  xlabel.size = 8,
  anno = FALSE,
  anno.tran_id = NULL,
  label.size = 2.5,
  y.upper.offset = 5
)

Arguments

MarvelObject	Marvel object. S3 object generated from CompareValues function.
method	Character string. The statistical method used for differential splicing analysis.
pval	Numeric value. Adjusted p-value below which the splcing event are considered as statistically significant and will consequently be color-annotated on the plot.
delta	Numeric value. The positive (and negative) value specified above (and below) which the splicing events 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.
xlabel.size	Numeric value. Font size of the xtick labels. Default is 8.
anno	Logical value. If set to TRUE, the specific gene names will be annotated on the plot. Speficified together with anno.tran_id.
anno.tran_id	Vector of character strings. When anno set to TRUE, the coordinates of the splicing events 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.

Value

An object of class S3 containing with new slot MarvelObject$DE$PSI$Plot[["method"]].

Examples

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

marvel.demo <- PlotDEValues.PSI.Mean(MarvelObject=marvel.demo,
                                     method="ad",
                                     pval=0.10,
                                     delta=5
                                     )

# Check output
marvel.demo$DE$PSI$Plot[["ad"]]

MARVEL documentation built on Oct. 31, 2022, 5:07 p.m.