vignettes/examples/track-tooltip-display.Rmd
track-tooltip-display.RmdTooltip can be specified by supplying a data frame when constructing the track and it can be modified after the track is constructed.
By default, when constructing a track from GRanges/IRanges, the tooltip is converted from the “meta-columns” of GRanges/IRanges, i.e. mcols(d).
suppressPackageStartupMessages({
library(TnT)
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
})
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGeneClick on the block to see the tooltip.
myIRanges <- IRanges(c(10, 100, 1000), width = c(30, 50, 500))
mytooltip <- as.data.frame(myIRanges)
myTrack <- TnT::BlockTrack(myIRanges, tooltip = mytooltip)
#TnTBoard(myTrack, IRanges(1, 2000))
TnTBoard(myTrack, GRanges("UnKnown", IRanges(1, 2000)))## - Missing argument `coord.range` and seqlength is unknown:
## automatically set coordinate limit to -309..1818 ...## Warning in readLines(con): incomplete final line found on '/home/jialin/R/
## x86_64-suse-linux-gnu-library/3.4/TnT/htmlwidgets/trackWidget.yaml'First, construct a gene track from the TxDb object.
geneTrack <- TnT::GeneTrackFromTxDb(txdb, height = 300)We can extract and replace the tooltip with tooltip and tooltip<-. In this case, we use the organism database to find the corresponding gene names of every gene, then add them to the tooltip.
head(df.tooltip <- TnT::tooltip(geneTrack))## gene_id
## 1 1
## 2 10
## 3 100
## 4 1000
## 5 10000
## 6 100008586genename <- AnnotationDbi::select(org.Hs.eg.db, as.character(df.tooltip$gene_id),
columns = "SYMBOL", keytype = "ENTREZID")## 'select()' returned 1:1 mapping between keys and columnsdf.tooltip$gene_symbol <- genename$SYMBOL[match(df.tooltip$gene_id, genename$ENTREZID)]
TnT::tooltip(geneTrack) <- df.tooltip
head(TnT::tooltip(geneTrack))## gene_id gene_symbol
## 1 1 A1BG
## 2 10 NAT2
## 3 100 ADA
## 4 1000 CDH2
## 5 10000 AKT3
## 6 100008586 GAGE12FWe can also modify the label to show gene symbol instead of entrez ID.
geneTrack$display_label <- TnT::strandlabel(TnT::tooltip(geneTrack)$gene_symbol,
strand(TnT::trackData(geneTrack)))Click to see the tooltip.
TnTGenome(geneTrack, GRanges("chrX", IRanges(100000, 10000000)))## Warning in readLines(con): incomplete final line found on '/home/jialin/R/
## x86_64-suse-linux-gnu-library/3.4/TnT/htmlwidgets/trackWidget.yaml'Columns of empty strings will be regarded as subsection titles, for example:
head(df.tooltip)## gene_id gene_symbol
## 1 1 A1BG
## 2 10 NAT2
## 3 100 ADA
## 4 1000 CDH2
## 5 10000 AKT3
## 6 100008586 GAGE12Fdf.tooltip <- cbind(
data.frame(`Identity` = ""),
df.tooltip[c("gene_id", "gene_symbol")]
)Click to see.
TnT::tooltip(geneTrack) <- df.tooltip
TnTGenome(geneTrack, GRanges("chrX", IRanges(100000, 10000000)))## 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] org.Hs.eg.db_3.4.1
## [2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [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] 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] pkgconfig_2.0.1 crayon_1.3.4
## [47] Matrix_1.2-10 MASS_7.3-47
## [49] xml2_1.1.1 prettyunits_1.0.2
## [51] assertthat_0.2.0 rmarkdown_1.9
## [53] roxygen2_6.0.1 httr_1.3.1
## [55] R6_2.2.2 GenomicAlignments_1.14.2
## [57] compiler_3.4.1