Description Usage Arguments Details Value Examples
VariantTrack
creates an IGV
track for VCF (variant call format) objects, either local or at a remote url
1 2 3 4 5 6 7 8 9 10 11 | VariantTrack(
trackName,
vcf,
trackHeight = 50,
anchorColor = "pink",
homvarColor = "rgb(17,248,254)",
hetvarColor = "rgb(34,12,253)",
homrefColor = "rgb(200,200,200)",
displayMode = "EXPANDED",
visibilityWindow = 1e+05
)
|
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
vcf |
A VCF object from the VariantAnnotation package, or a list(url=x, index=y) pointing to a vcf file |
trackHeight |
track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files) |
anchorColor |
CSS color name (e.g., "red" or "#FF0000") for the "anchoring" graphical segment in the track |
homvarColor |
CSS color name for homozygous variant samples, rgb(17,248,254) by default (~turquoise) |
hetvarColor |
CSS color name for heterzygous variant samples, rgb(34,12,253) by default (~royalBlue) |
homrefColor |
CSS color names for homozygous reference samples, rgb(200,200,200) by default (~lightGray) |
displayMode |
"COLLAPSED", "EXPANDED", or "SQUISHED" |
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 VariantTrack object
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | #----------------------------
# first, from a local file
#----------------------------
f <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
roi <- GRanges(seqnames="22", ranges=IRanges(start=c(50301422, 50989541),
end=c(50312106, 51001328),
names=c("gene_79087", "gene_644186")))
vcf.sub <- VariantAnnotation::readVcf(f, "hg19", param=roi)
track.local <- VariantTrack("chr22-tiny", vcf.sub)
#----------------------------
# now try a url track
#----------------------------
data.url <- sprintf("%s/%s", "https://s3.amazonaws.com/1000genomes/release/20130502",
"ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz")
index.url <- sprintf("%s.tbi", data.url)
url <- list(data=data.url, index=index.url)
track.url <- VariantTrack("1kg", url)
|
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