plotSplicingEvent: Plot diagram of alternative splicing events

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Plot diagram of alternative splicing events

Description

Plot diagram of alternative splicing events

Usage

plotSplicingEvent(
  ASevent,
  data = NULL,
  showText = TRUE,
  showPath = TRUE,
  showAlternative1 = TRUE,
  showAlternative2 = TRUE,
  constitutiveWidth = NULL,
  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

events <- c(
  "A3SS_15_+_63353138_63353912_63353397_TPM1",
  "A3SS_11_-_61118463_61117115_61117894_CYB561A3",
  "A5SS_21_+_48055675_48056459_48056808_PRMT2",
  "A5SS_1_-_1274742_1274667_1274033_DVL1",
  "AFE_9_+_131902430_131901928_131904724_PPP2R4",
  "AFE_5_-_134686513_134688636_134681747_H2AFY",
  "ALE_12_+_56554104_56554410_56555171_MYL6",
  "ALE_8_-_38314874_38287466_38285953_FGFR1",
  "SE_9_+_6486925_6492303_6492401_6493826_UHRF2",
  "SE_19_-_5218431_5216778_5216731_5215606_PTPRS",
  "MXE_15_+_63335142_63335905_63336030_63336226_63336351_63349184_TPM1",
  "MXE_17_-_74090495_74087316_74087224_74086478_74086410_74085401_EXOC7")
diagram <- plotSplicingEvent(events)

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

## End(Not run)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.