plotSplicingEvent {psichomics} | R Documentation

## 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)

[Package psichomics version 1.18.6 Index]