plotSplicingEvent {psichomics} | R Documentation

## Plot diagram of alternative splicing events

### Description

Plot diagram of alternative splicing events

### Usage

    plotSplicingEvent(
      ASevent,
      class = NULL,
      style = NULL,
      showText = TRUE,
      showPath = TRUE,
      showAlternative1 = TRUE,
      showAlternative2 = TRUE,
      constitutiveWidth = 60,
      alternativeWidth = NULL,
      intronWidth = 15,
      constitutiveFill = "lightgray",
      constitutiveStroke = "darkgray",
      alternative1Fill = "#ffb153",
      alternative1Stroke = "#faa000",
      alternative2Fill = "#caa06c",
      alternative2Stroke = "#9d7039"
    )

### Arguments

`ASevent` | Character: alternative splicing event identifiers
`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

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]]
    diagram

[Package psichomics version 1.14.1 Index]