GWASUrlTrack | R Documentation |
GWASUrlTrack
creates an IGV
manhattan track GWAS data
GWASUrlTrack( trackName, url, chrom.col, pos.col, pval.col, color = "darkBlue", trackHeight = 50, visibilityWindow = 1e+05 )
trackName |
A character string, used as track label by igv, we recommend unique names per track. |
url |
character |
chrom.col |
numeric, the column number of the chromosome column |
pos.col |
numeric, the column number of the position column |
pval.col |
numeric, the column number of the GWAS pvalue colum |
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 GWASUrlTrack object
track <- GWASUrlTrack("GWAS from url", "https://s3.amazonaws.com/igv.org.demo/gwas_sample.tsv.gz", chrom.col=12, pos.col=13, pval.col=28) # note: this track is autoscaled. apparently some infinite values in the file, # leading to a flat, low track. reproduce this in static html, report issue to igv.js # temporary workaround: use the interactive track gear to set display range. if(interactive()){ igv <- igvR() setGenome(igv, "hg38") setBrowserWindowTitle(igv, "GWAS URL demo") displayTrack(igv, track) }
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