igvR 1.18.1
With the popularity and wide availability of Hi-C data - a high throughput chromatin confirmation capture technology - an appropriate display format was needed. The igv.js team created the Interact track, supporint the bedpe data file format.
We demonstrate this track with a few lines extracted from the Encode project’s ENCFF110BUX experiment, from Michael Snyder’s lab, showing the boundaries and extent of two topologically-associated domains (TADS), typically small genomic regions which are somewhat isolated from neighboring regions, which is believed to play a role in restricting enhancer/promoter interactions.
An equally important, and perhaps more common use of paired-end interaction data is to represent Hi-C maps of enhancer-promoter interactions. These data also rely upon the bedpe file format.
igv.js provides several visualization parameters not yet supported in igvR.
To define a TAD, two genomic locations are required, as shown here and in the code below:
chrom1 start1 end1 chrom2 start2 end2
2 105780000 105790000 2 105890000 105900000
2 105575000 105600000 2 106075000 106100000
These few lines provide a complete, if minimal introduction to the BedpeInteractionsTrack.
library(igvR)
igv <- igvR()
setBrowserWindowTitle(igv, "Paired-end demo")
setGenome(igv, "hg38")
tbl.bedpe <- data.frame(chrom1=c("2","2"),
start1=c(105780000, 105575000),
end1=c(105790000, 105600000),
chrom2=c("2","2"),
start2=c(105890000, 106075000),
end2=c(105900000, 106100000),
stringsAsFactors=FALSE)
# construct a "region of interest" (roi) string from tbl.bedpe
# this is where our two features are found.
shoulder <- 300000
roi <- sprintf("%s:%d-%d", tbl.bedpe$chrom1[1],
min(tbl.bedpe$start1) - shoulder,
max(tbl.bedpe$end2) + shoulder)
showGenomicRegion(igv, roi)
track <- BedpeInteractionsTrack("ENCFF110BUX", tbl.bedpe)
displayTrack(igv, track)
sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Ventura 13.0
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#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
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#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
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#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
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#> other attached packages:
#> [1] BiocStyle_2.26.0
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#> loaded via a namespace (and not attached):
#> [1] bookdown_0.32 digest_0.6.31 R6_2.5.1 lifecycle_1.0.3 jsonlite_1.8.4
#> [6] magrittr_2.0.3 evaluate_0.20 highr_0.10 stringi_1.7.12 cachem_1.0.6
#> [11] rlang_1.0.6 cli_3.6.0 jquerylib_0.1.4 bslib_0.4.2 vctrs_0.5.1
#> [16] rmarkdown_2.20 tools_4.2.2 stringr_1.5.0 glue_1.6.2 xfun_0.36
#> [21] yaml_2.3.6 fastmap_1.1.0 compiler_4.2.2 BiocManager_1.30.19 htmltools_0.5.4
#> [26] knitr_1.41 sass_0.4.4