BedpeInteractionsTrack-class {igvR} | R Documentation |
BedpeInteractionsTrack
creates an IGV
track for two-location annotations
BedpeInteractionsTrack( trackName, table, color = "darkBlue", trackHeight = 50, displayMode = "EXPANDED", visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
color |
A css color name (e.g., "red" or "#FF0000" |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
visibilityWindow |
Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types. |
A BedpeInteractionsTrack object
#---------------------------- # first, from a local file #---------------------------- file <- system.file(package="igvR", "extdata", "sixColumn-demo1.bedpe") tbl.bedpe <- read.table(file, sep="\t", as.is=TRUE, header=TRUE) dim(tbl.bedpe) # 32 6 track <- BedpeInteractionsTrack("bedpe-6", tbl.bedpe) #------------------------------------------ # show the relevant portion of the genome #------------------------------------------ shoulder <- 10000 roi <- with(tbl.bedpe, sprintf("%s:%d-%d", chrom1[1], min(start1)-shoulder, max(end2) + shoulder)) # showGenomicRegion(igv, roi) # displayTrack(igv, track)