plotSplicingEvent: Plot diagram of alternative splicing events

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

Description

Plot diagram of alternative splicing events

Usage

plotSplicingEvent(
  ASevent,
  data = 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",
  class = NULL,
  style = NULL
)

Arguments

ASevent	Character: alternative splicing event identifiers
data	Matrix or data frame: alternative splicing information
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
class	Character: class of SVG parent tag
style	Character: style of SVG parent tag

Value

List of SVG (one for each alternative splicing event)

Examples

ASevent <- c(
    "SE_9_+_6486925_6492303_6492401_6493826_UHRF2",
    "SE_11_+_86925_92303_92401_93826_TESTING/MHG2",
    "A5SS_15_+_63353472_63353987_63354414_TPM1",
    "A3SS_3_-_145796903_145794682_145795711_PLOD2",
    "AFE_17_-_15165746_15168471_15164078_PMP22",
    "ALE_18_-_5395066_5394792_5393477_EPB41L3",
    "MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1")
diagram <- plotSplicingEvent(ASevent)

diagram[["A3SS_3_-_145796903_145794682_145795711_PLOD2"]]
diagram[[6]]
## Not run: diagram

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