vignettes/examples/tracktype-GeneTrack.Rmd
tracktype-GeneTrack.RmdThis page describes how to construct a GeneTrack/FeatureTrack from TxDb or GRanges.
suppressPackageStartupMessages({
library(TnT)
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(EnsDb.Hsapiens.v75)
})A GeneTrack can be easily constructed from a TxDb.
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
gtrack <- TnT::GeneTrackFromTxDb(txdb)
gtrack## A GeneTrack
## | Label: txdb
## | Background: missing, use 'white'
## | Height: 100
## | Data: GeneTrackData object with 23056 ranges and 5 metadata columns:
## | seqnames ranges strand | tooltip color
## | <Rle> <IRanges> <Rle> | <data.frame> <character>
## | 1 chr19 [ 58858172, 58874214] - | 1 black
## | 10 chr8 [ 18248755, 18258723] + | 10 black
## | 100 chr20 [ 43248163, 43280376] - | 100 black
## | 1000 chr18 [ 25530930, 25757445] - | 1000 black
## | 10000 chr1 [243651535, 244006886] - | 10000 black
## | ... ... ... ... . ... ...
## | 9991 chr9 [114979995, 115095944] - | 9991 black
## | 9992 chr21 [ 35736323, 35743440] + | 9992 black
## | 9993 chr22 [ 19023795, 19109967] - | 9993 black
## | 9994 chr6 [ 90539619, 90584155] + | 9994 black
## | 9997 chr22 [ 50961997, 50964905] - | 9997 black
## | key display_label id
## | <integer> <character> <character>
## | 1 1 < 1 1
## | 10 2 10 > 10
## | 100 3 < 100 100
## | 1000 4 < 1000 1000
## | 10000 5 < 10000 10000
## | ... ... ... ...
## | 9991 23052 < 9991 9991
## | 9992 23053 9992 > 9992
## | 9993 23054 < 9993 9993
## | 9994 23055 9994 > 9994
## | 9997 23056 < 9997 9997
## | -------
## | seqinfo: 93 sequences (1 circular) from hg19 genomeTo show the track, put the track into a TnTBoard or TnTGenome, optionally specifing the view range with a GRanges object.
TnTGenome(gtrack, view.range = GRanges("chr13", IRanges(32889617, 32973809)) * 0.7)## Warning in readLines(con): incomplete final line found on '/home/jialin/R/
## x86_64-suse-linux-gnu-library/3.4/TnT/htmlwidgets/trackWidget.yaml'FeatureTrack is an alias of GeneTrack, in the sense that this display method can be applied to general overlapping genomic features.
Function FeatureTrack can construct a GeneTrack/FeatureTrack from a GRanges object, and gives you more control of the display (i.e. color, feature labels, tooltip).
For example, we first extract the genes as a GRanges object from a EnsDb.
gene <- genes(EnsDb.Hsapiens.v75)
head(gene)## GRanges object with 6 ranges and 6 metadata columns:
## seqnames ranges strand | gene_id
## <Rle> <IRanges> <Rle> | <character>
## ENSG00000223972 1 [11869, 14412] + | ENSG00000223972
## ENSG00000227232 1 [14363, 29806] - | ENSG00000227232
## ENSG00000243485 1 [29554, 31109] + | ENSG00000243485
## ENSG00000237613 1 [34554, 36081] - | ENSG00000237613
## ENSG00000268020 1 [52473, 54936] + | ENSG00000268020
## ENSG00000240361 1 [62948, 63887] + | ENSG00000240361
## gene_name gene_biotype seq_coord_system symbol
## <character> <character> <character> <character>
## ENSG00000223972 DDX11L1 pseudogene chromosome DDX11L1
## ENSG00000227232 WASH7P pseudogene chromosome WASH7P
## ENSG00000243485 MIR1302-10 lincRNA chromosome MIR1302-10
## ENSG00000237613 FAM138A lincRNA chromosome FAM138A
## ENSG00000268020 OR4G4P pseudogene chromosome OR4G4P
## ENSG00000240361 OR4G11P pseudogene chromosome OR4G11P
## entrezid
## <list>
## ENSG00000223972 100287596,100287102
## ENSG00000227232 100287171,653635
## ENSG00000243485 100422919,100422834,100422831,...
## ENSG00000237613 654835,645520,641702
## ENSG00000268020 NA
## ENSG00000240361 NA
## -------
## seqinfo: 273 sequences from GRCh37 genomeThen we construct the GeneTrack using this GRanges object with FeatureTrack, specifing our custom feature labels, feature colors and tooltips. Finally show the track with TnTGenome.
ensGeneTrack <- TnT::FeatureTrack(gene, tooltip = as.data.frame(gene),
names = paste(gene$symbol, " (", gene$gene_biotype, ")", sep = ""),
color = TnT::mapcol(gene$gene_biotype, palette.fun = grDevices::rainbow))
TnTGenome(ensGeneTrack, view.range = gene[gene$symbol == "BRCA2"][1] * .7)## 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] EnsDb.Hsapiens.v75_2.99.0
## [2] ensembldb_2.1.13
## [3] AnnotationFilter_1.1.9
## [4] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [5] GenomicFeatures_1.30.3
## [6] AnnotationDbi_1.40.0
## [7] Biobase_2.38.0
## [8] TnT_1.3.1
## [9] GenomicRanges_1.30.3
## [10] GenomeInfoDb_1.14.0
## [11] IRanges_2.12.0
## [12] S4Vectors_0.16.0
## [13] BiocGenerics_0.24.0
##
## loaded via a namespace (and not attached):
## [1] httr_1.3.1 RMySQL_0.10.14
## [3] bit64_0.9-7 jsonlite_1.5
## [5] AnnotationHub_2.9.17 shiny_1.0.5
## [7] assertthat_0.2.0 interactiveDisplayBase_1.15.0
## [9] blob_1.1.1 GenomeInfoDbData_1.0.0
## [11] Rsamtools_1.30.0 yaml_2.1.19
## [13] progress_1.1.2 RSQLite_2.1.0
## [15] backports_1.1.2-9000 lattice_0.20-35
## [17] digest_0.6.15 XVector_0.18.0
## [19] colorspace_1.3-2 htmltools_0.3.6
## [21] httpuv_1.3.6.2 Matrix_1.2-10
## [23] XML_3.98-1.10 pkgconfig_2.0.1
## [25] biomaRt_2.34.2 zlibbioc_1.24.0
## [27] xtable_1.8-2 BiocParallel_1.12.0
## [29] SummarizedExperiment_1.8.1 lazyeval_0.2.1
## [31] magrittr_1.5 crayon_1.3.4
## [33] mime_0.5 memoise_1.1.0
## [35] evaluate_0.10.1 fs_1.2.2
## [37] MASS_7.3-47 xml2_1.1.1
## [39] BiocInstaller_1.28.0 tools_3.4.1
## [41] prettyunits_1.0.2 matrixStats_0.52.2
## [43] stringr_1.3.0 DelayedArray_0.4.1
## [45] Biostrings_2.46.0 compiler_3.4.1
## [47] pkgdown_1.0.0 rlang_0.2.0.9001
## [49] grid_3.4.1 RCurl_1.95-4.10
## [51] htmlwidgets_1.2 bitops_1.0-6
## [53] rmarkdown_1.9 curl_3.2
## [55] DBI_0.8 roxygen2_6.0.1
## [57] R6_2.2.2 GenomicAlignments_1.14.2
## [59] knitr_1.20 rtracklayer_1.38.3
## [61] bit_1.1-12 commonmark_1.4
## [63] rprojroot_1.3-2 ProtGenerics_1.9.1
## [65] desc_1.2.0 stringi_1.2.2
## [67] Rcpp_0.12.16