diagramSplicingEvent: Prepare SVG diagram of alternative splicing events

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Description

Prepare SVG diagram of alternative splicing events

Usage

diagramSplicingEvent(
  parsed,
  type,
  class = "pull-right",
  style = NULL,
  showText = TRUE,
  showPath = TRUE,
  showAlternative1 = TRUE,
  showAlternative2 = TRUE,
  constitutiveWidth = 60,
  alternativeWidth = NULL,
  intronWidth = NULL,
  constitutiveFill = "lightgray",
  constitutiveStroke = "darkgray",
  alternative1Fill = "#ffb153",
  alternative1Stroke = "#faa000",
  alternative2Fill = "#caa06c",
  alternative2Stroke = "#9d7039"
)

Arguments

parsed	Alternative splicing event
type	Character: alternative splicing event type
class	Character: class of SVG parent tag
style	Character: style of SVG parent tag
showText	Boolean: display coordinates and length (if available)
showPath	Boolean: display alternative splicing junctions
showAlternative1	Boolean: show alternative exon 1 and respective splicing junctions and text?
showAlternative2	Boolean: show alternative exon 2 and respective splicing junctions and text? (only related with mutually exclusive exons)
constitutiveWidth	Numeric: width of constitutive exon(s)
alternativeWidth	Numeric: width of alternative exon(s)
intronWidth	Numeric: width of intron's representation
constitutiveFill	Character: fill colour of constitutive exons
constitutiveStroke	Character: stroke colour of constitutive exons
alternative1Fill	Character: fill colour of alternative exon 1
alternative1Stroke	Character: stroke colour of alternative exon 1
alternative2Fill	Character: fill colour of alternative exon 2
alternative2Stroke	Character: stroke colour of alternative exon 2

Value

Diagrams per alternative splicing event in SVG

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.