MARVEL (version 1.4.0)

PlotDEValues.PSI.Distance: Plot differential splicing analysis results based on distance statistics.

Description

Ranked plot for differential splicing analysis results based on distance statistics. Only statistical test that assess the overall PSI distribution between two cell groups will be eligible for plotting here, e.g., Anderson-Darling and DTS. x-axis represents the distance statistics. y-axis represents the adjusted p-values.

Usage

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

Value

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

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 events are considered as 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.

Examples

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

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

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