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

This is the low-level util to create visualizations.

expose_all <- function (package) {
    attachname <- paste0(package, "_all")
    while (attachname %in% search()) detach(attachname, character.only = TRUE)
    pkgns <- loadNamespace(package)
    attach(pkgns, name = attachname)
    invisible(pkgns)
}
suppressMessages(expose_all("TnT"))

Create a TnT Board with Literal JavaScript

trackWidget('
    var axisTrack = tnt.board.track()
        .height(20)
        .color("white")
        .display(tnt.board.track.feature.axis());

    var blockTrack = tnt.board.track()
        .height(30)
        .color("grey")
        .data(tnt.board.track.data.sync()
            .retriever(function () {
                return [
                    {start: 200, end: 350},
                    {start: 400, end: 450}
                ]
            })
        )
        .display(
            tnt.board.track.feature.block()
            .color("red")
        );

    var board = tnt.board()
        .from(100)
        .to(500)
        .min(0)
        .max(1000)
        .add_track(axisTrack)
        .add_track(blockTrack);
    board
')

Create a TnT Board with JSCascade Util Functions

axisTrack <- jc(
    tnt.board.track = ma(),
    height = 20,
    color = "white",
    display = jc(tnt.board.track.feature.axis = ma())
)
blockTrack <- jc(
    tnt.board.track = ma(),
    height = 30,
    color = "green",
    data = jc(
        tnt.board.track.data.sync = ma(),
        retriever = js("function() {
            return [
                {start: 200, end: 350},
                {start: 550, end: 770}
            ];
        }")
    ),
    display = jc(
        tnt.board.track.feature.block = ma(),
        color = "red",
        index = js("function (d) {return d.start}")
    )
)
tntdef <- jc(
    tnt.board = ma(),
    from = 0,
    to = 500,
    min = 0,
    max = 1000,
    add_track = axisTrack,
    add_track = blockTrack
)
asJS(tntdef)
trackWidget(tntdef)

genome <- jc(
    tnt.board.genome = ma(),
    species = "human",
    chr = 10,
    from = 410000,
    to = 420000,
    min_coord = js("new Promise(function (res) {res(-10000)})"),
    max_coord = js("new Promise(function (res) {res(420000)})")
)
trackWidget(genome)

Session Info

sessionInfo()

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