UCSCBedAnnotationTrack-class | R Documentation |
UCSCBedAnnotationTrack
creates and IGV
track for bed objects imported using rtracklayer
UCSCBedAnnotationTrack( trackName, annotation, color = "darkGrey", displayMode = "SQUISHED", trackHeight = 50, expandedRowHeight = 30, squishedRowHeight = 15, maxRows = 500, searchable = FALSE, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
annotation |
A UCSCData object imported by |
color |
A CSS color name (e.g., "red" or "#FF0000") |
displayMode |
"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise. |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
expandedRowHeight |
Height of each row of features in "EXPANDED" mode. |
squishedRowHeight |
Height of each row of features in "SQUISHED" mode, for compact viewing. |
maxRows |
of features to display |
searchable |
If TRUE, labels on annotation elements may be used in search |
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. |
Detailed description goes here
A UCSCBedAnnotationTrack object
bed.filepath <- system.file(package = "rtracklayer", "tests", "test.bed") gr.bed <- rtracklayer::import(bed.filepath) track <- UCSCBedAnnotationTrack("UCSC bed", gr.bed, color="blue", displayMode="SQUISHED") if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "UCSC bed10 demo") showGenomicRegion(igv, "chr7:127,469,879-127,476,276") displayTrack(igv, track) }
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