A block track can be created from a GRanges or IRanges object, showing the coverage of a Range-like object.
suppressPackageStartupMessages({
library(TnT)
library(GenomicFeatures)
})
set.seed(42)Construct a IRanges object and a GRanges object.
ir <- IRanges(start = c(69, 420, 6942), width = c(10, 100, 1000))
gr <- GRanges("chr12", ir)To construct the track and create the visualization.
btrack <- TnT::BlockTrack(gr, tooltip = as.data.frame(gr),
label = "My GRanges", color = "yellow")
TnT::TnTBoard(btrack, range(gr))## - Missing argument `coord.range` and seqlength is unknown:
## automatically set coordinate limit to -1618..9628 ...## Warning in readLines(con): incomplete final line found on '/home/jialin/R/
## x86_64-suse-linux-gnu-library/3.4/TnT/htmlwidgets/trackWidget.yaml'sessionInfo()## R version 3.4.1 (2017-06-30)
## Platform: x86_64-suse-linux-gnu (64-bit)
## Running under: openSUSE Tumbleweed
##
## Matrix products: default
## BLAS: /usr/lib64/R/lib/libRblas.so
## LAPACK: /usr/lib64/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 methods stats graphics grDevices utils
## [8] datasets base
##
## other attached packages:
## [1] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0 Biobase_2.38.0
## [4] TnT_1.3.1 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0
## [7] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0
##
## loaded via a namespace (and not attached):
## [1] SummarizedExperiment_1.8.1 progress_1.1.2
## [3] lattice_0.20-35 colorspace_1.3-2
## [5] htmltools_0.3.6 rtracklayer_1.38.3
## [7] yaml_2.1.19 blob_1.1.1
## [9] XML_3.98-1.10 rlang_0.2.0.9001
## [11] pkgdown_1.0.0 DBI_0.8
## [13] BiocParallel_1.12.0 bit64_0.9-7
## [15] matrixStats_0.52.2 GenomeInfoDbData_1.0.0
## [17] stringr_1.3.0 zlibbioc_1.24.0
## [19] Biostrings_2.46.0 commonmark_1.4
## [21] htmlwidgets_1.2 memoise_1.1.0
## [23] evaluate_0.10.1 knitr_1.20
## [25] biomaRt_2.34.2 Rcpp_0.12.16
## [27] backports_1.1.2-9000 DelayedArray_0.4.1
## [29] desc_1.2.0 jsonlite_1.5
## [31] XVector_0.18.0 fs_1.2.2
## [33] bit_1.1-12 Rsamtools_1.30.0
## [35] RMySQL_0.10.14 digest_0.6.15
## [37] stringi_1.2.2 grid_3.4.1
## [39] rprojroot_1.3-2 tools_3.4.1
## [41] bitops_1.0-6 magrittr_1.5
## [43] RCurl_1.95-4.10 RSQLite_2.1.0
## [45] crayon_1.3.4 Matrix_1.2-10
## [47] MASS_7.3-47 xml2_1.1.1
## [49] prettyunits_1.0.2 assertthat_0.2.0
## [51] rmarkdown_1.9 roxygen2_6.0.1
## [53] httr_1.3.1 R6_2.2.2
## [55] GenomicAlignments_1.14.2 compiler_3.4.1