Composite track is a way to combine multiple types of features into one track. A composite track can be constructed by combining a list of different tracks with function merge.
Label, background and height of the composite track will be derived from the component tracks and can be further accessed and modified with trackSpec and trackSpec<-.
suppressPackageStartupMessages({
library(TnT)
library(GenomicFeatures)
library(AnnotationHub)
})
set.seed(42)First to construct a block track and a pin track from data.
gr <- GRanges("chr1", IRanges(c(11000, 20000, 60000), width = 2000))
gpos <- GRanges("chr1", IRanges(c(12000, 21000, 61000), width = 1), value = c(1, 2, 3))
btrack <- TnT::BlockTrack(gr, label = "Block Track", tooltip = as.data.frame(gr), color = "lightblue4")
ptrack <- TnT::PinTrack(gpos, label = "Pin Track", tooltip = as.data.frame(gpos), background = "beige")Then use merge to construct a composite track and showing it.
ctrack <- TnT::merge(btrack, ptrack)
TnTBoard(ctrack)## - Missing argument `view.range`:
## automatically select 4625..68374 on seqlevel chr1...## - Missing argument `coord.range` and seqlength is unknown:
## automatically set coordinate limit to 71..72927 ...## Warning in readLines(con): incomplete final line found on '/home/jialin/R/
## x86_64-suse-linux-gnu-library/3.4/TnT/htmlwidgets/trackWidget.yaml'Be aware that the components in a composite track are rendered according to the order in merge. For example, the block track will cover the pin track if we switch the order.
TnTBoard(merge(ptrack, btrack)) # the pin track has been covered## - Missing argument `view.range`:
## automatically select 4625..68374 on seqlevel chr1...## - Missing argument `coord.range` and seqlength is unknown:
## automatically set coordinate limit to 71..72927 ...## Warning in readLines(con): incomplete final line found on '/home/jialin/R/
## x86_64-suse-linux-gnu-library/3.4/TnT/htmlwidgets/trackWidget.yaml'Show all three tracks and add axis indicator.
TnTGenome(list(ctrack, ptrack, btrack))## - Missing argument `view.range`:
## automatically select 5875..67125 on seqlevel chr1...## - Missing argument `coord.range` and seqlength is unknown:
## automatically set coordinate limit to 71..72927 ...## Warning in readLines(con): incomplete final line found on '/home/jialin/R/
## x86_64-suse-linux-gnu-library/3.4/TnT/htmlwidgets/trackWidget.yaml'library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
gtrack <- TnT::GeneTrackFromTxDb(txdb, label = "Gene", color = "burlywood3")
ah <- AnnotationHub()## snapshotDate(): 2017-10-27ah <- query(ah, "cpgisland")
cpg <- ah[[names(ah[ah$genome == "hg19"])]]## loading from cache '/home/jialin//.AnnotationHub/5086'cpgtrack <- TnT::BlockTrack(cpg, label = "CpG Islands", tooltip = as.data.frame(cpg),
color = "lightblue")
TnTGenome(merge(cpgtrack, gtrack),
view.range = GRanges("chr1", IRanges(84884317, 85205497)))## 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] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [2] AnnotationHub_2.9.17
## [3] GenomicFeatures_1.30.3
## [4] AnnotationDbi_1.40.0
## [5] Biobase_2.38.0
## [6] TnT_1.3.1
## [7] GenomicRanges_1.30.3
## [8] GenomeInfoDb_1.14.0
## [9] IRanges_2.12.0
## [10] S4Vectors_0.16.0
## [11] BiocGenerics_0.24.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.16 lattice_0.20-35
## [3] prettyunits_1.0.2 Rsamtools_1.30.0
## [5] Biostrings_2.46.0 assertthat_0.2.0
## [7] rprojroot_1.3-2 digest_0.6.15
## [9] mime_0.5 R6_2.2.2
## [11] backports_1.1.2-9000 RSQLite_2.1.0
## [13] evaluate_0.10.1 BiocInstaller_1.28.0
## [15] httr_1.3.1 zlibbioc_1.24.0
## [17] rlang_0.2.0.9001 progress_1.1.2
## [19] curl_3.2 blob_1.1.1
## [21] Matrix_1.2-10 rmarkdown_1.9
## [23] pkgdown_1.0.0 desc_1.2.0
## [25] RMySQL_0.10.14 BiocParallel_1.12.0
## [27] stringr_1.3.0 htmlwidgets_1.2
## [29] RCurl_1.95-4.10 bit_1.1-12
## [31] biomaRt_2.34.2 shiny_1.0.5
## [33] DelayedArray_0.4.1 compiler_3.4.1
## [35] httpuv_1.3.6.2 rtracklayer_1.38.3
## [37] pkgconfig_2.0.1 htmltools_0.3.6
## [39] SummarizedExperiment_1.8.1 GenomeInfoDbData_1.0.0
## [41] interactiveDisplayBase_1.15.0 roxygen2_6.0.1
## [43] matrixStats_0.52.2 XML_3.98-1.10
## [45] crayon_1.3.4 GenomicAlignments_1.14.2
## [47] MASS_7.3-47 bitops_1.0-6
## [49] commonmark_1.4 grid_3.4.1
## [51] xtable_1.8-2 jsonlite_1.5
## [53] DBI_0.8 magrittr_1.5
## [55] stringi_1.2.2 XVector_0.18.0
## [57] fs_1.2.2 xml2_1.1.1
## [59] tools_3.4.1 bit64_0.9-7
## [61] yaml_2.1.19 colorspace_1.3-2
## [63] memoise_1.1.0 knitr_1.20