In Marlin-Na/TnT: Interactive Visualization for Genomic Features

Tooltip 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.knownGene

Basic Example using BlockTrack

Click 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)))

Modify Tooltip of a Constructed Track

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))

genename <- AnnotationDbi::select(org.Hs.eg.db, as.character(df.tooltip$gene_id),
                      columns = "SYMBOL", keytype = "ENTREZID")
df.tooltip$gene_symbol <- genename$SYMBOL[match(df.tooltip$gene_id, genename$ENTREZID)]
TnT::tooltip(geneTrack) <- df.tooltip
head(TnT::tooltip(geneTrack))

We 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)))

Use Sub-headers in Tooltip

Columns of empty strings will be regarded as subsection titles, for example:

head(df.tooltip)
df.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)))

Session Info

sessionInfo()

Marlin-Na/TnT documentation built on Jan. 31, 2020, 7:43 a.m.