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