PlotDEValues.PSI.Mean.g2vsg1 {MARVEL}

Plot differential splicing analysis results based on mean PSI difference

Description

Scatterplot of differential splicing analysis results based on mean PSI difference between 2 groups of cells. x-axis represents the mean PSI values of cell group 1. y-axis represents the mean PSI values of cell group 2.

Usage

PlotDEValues.PSI.Mean.g2vsg1(
  MarvelObject,
  method,
  pval,
  delta = 5,
  point.size = 1,
  xlabel.size = 8,
  anno = FALSE,
  anno.tran_id = NULL,
  label.size = 2.5,
  point.alpha = 1,
  event.types = c("SE", "MXE", "RI", "A5SS", "A3SS", "AFE", "ALE"),
  event.types.colors = NULL
)

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.

point.alpha

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

event.types

Vector of character string(s). The specific splicing event to plot. May take any one or more of the following values "SE", "MXE", "RI", "A5SS", "A3SS", "AFE", and "ALE".

event.types.colors

Vector of character string(s). Customise colors as per splicing event type specified in event.types option. Should be of same length as event.types option.

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.g2vsg1(MarvelObject=marvel.demo,
                                     method="ad",
                                     pval=0.10,
                                     delta=5
                                     )

# Check output
marvel.demo$DE$PSI$Plot
marvel.demo$DE$PSI$Summary