plotSplicingEvent {psichomics} | R Documentation |
Plot diagram of alternative splicing events
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" )
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 |
List of SVG (one for each alternative splicing event)
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