In Marlin-Na/TnT: Interactive Visualization for Genomic Features
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"))
Coverage Feature
https://github.com/tntvis/tnt.board/blob/master/examples/dynamic_ranges/ranges.js
trackWidget('
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{start:981,end:990,height:0.684219},
{start:991,end:1000,height:0.910972}
];
// The coverage custom feature
var coverageFeature = tnt.board.track.feature()
.index(function(d) {
return d.start + "-" + d.end;
});
var coverageFeatureInverse = tnt.board.track.feature()
.index(function(d) {
return d.start + "-" + d.end;
});
// Create new elements
coverageFeature.create(function (el) {
var xScale = coverageFeature.scale();
var track = this;
var y = track.height();
var barScale = d3.scale.linear()
.domain([0, 1])
.range([0, y]);
var colorScale = d3.scale.linear()
.domain([0, 1])
.range(["#5ba633", "#027be3"]);
var g = el
.append("g");
g.append("rect")
.attr("x", function (d) {
return xScale(d.start);
})
.attr("y", function (d) {
return y - barScale(d.height);
//return 0;
})
.attr("width", function (d) {
return xScale(d.end) - xScale(d.start);
})
.attr("height", function (d) {
return barScale(d.height);
})
.style("fill", function (d) {
return colorScale(d.height);
})
});
coverageFeatureInverse.create(function (el) {
var xScale = coverageFeature.scale();
var track = this;
var y = track.height();
var barScale = d3.scale.linear()
.domain([0, 1])
.range([0, y]);
var colorScale = d3.scale.linear()
.domain([0, 1])
.range(["#5ba633", "#027be3"]);
var g = el
.append("g");
g.append("rect")
.attr("x", function (d) {
return xScale(d.start);
})
.attr("y", function (d) {
//return y - barScale(d.height);
return 0;
})
.attr("width", function (d) {
return xScale(d.end) - xScale(d.start);
})
.attr("height", function (d) {
return barScale(d.height);
})
.style("fill", function (d) {
return colorScale(d.height);
})
});
coverageFeature.move(function (el) {
var xScale = coverageFeature.scale();
el.select("g")
.select("rect")
.attr("x", function (d) {
return xScale(d.start);
})
.attr("width", function (d) {
return xScale(d.end) - xScale(d.start);
})
});
coverageFeatureInverse.move(function (el) {
var xScale = coverageFeature.scale();
el.select("g")
.select("rect")
.attr("x", function (d) {
return xScale(d.start);
})
.attr("width", function (d) {
return xScale(d.end) - xScale(d.start);
})
});
// The board
var myBoard = tnt.board().from(20).to(500).max(1000);
// The location track
var location_track = tnt.board.track()
.height(20)
.color("white")
.display(tnt.board.track.feature.axis()
.orientation("top")
);
// The ranges track
var ranges_track = tnt.board.track()
.label("coverage plot")
.height(80)
.color("white")
.data (tnt.board.track.data.sync()
.retriever (function (loc) {
// Return only the range on display
var rangeData = data.filter(function (d) {
return (d.start > loc.from) && (d.end < loc.to);
});
// if necessary group or edit the number of elements to show
// rangeData = getNewRange(data, loc)
return rangeData;
})
)
.display(coverageFeature);
var ranges_track2 = tnt.board.track()
.label("coverage plot")
.height(80)
.color("white")
.data (tnt.board.track.data.sync()
.retriever (function (loc) {
// Return only the range on display
var rangeData = data.filter(function (d) {
return (d.start > loc.from) && (d.end < loc.to);
});
// if necessary group or edit the number of elements to show
// rangeData = getNewRange(data, loc)
return rangeData;
})
)
.display(coverageFeatureInverse);
// Add the tracks and start
myBoard
.add_track(location_track)
.add_track(ranges_track2)
.add_track(ranges_track);
myBoard
//myBoard(document.getElementById("mydiv"));
//myBoard.start();
')
2
trackWidget('
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{start: 999, end: 999, height: 0.347196},
{start: 1000, end: 1000, height: 0.532514}
];
// The coverage custom feature
var coverageFeature = tnt.board.track.feature()
.index(function(d) {
return d.start + "-" + d.end;
});
// Create new elements
coverageFeature.create(function (el) {
var xScale = coverageFeature.scale();
var track = this;
var y = track.height();
var barScale = d3.scale.linear()
.domain([0, 1])
.range([0, y]);
var colorScale = d3.scale.linear()
.domain([0, 1])
.range(["#5ba633", "#027be3"]);
var g = el
.append("g");
g.append("rect")
.attr("x", function (d) {
return xScale(d.start);
})
.attr("y", function (d) {
return y - barScale(d.height);
})
.attr("width", function (d) {
return xScale(d.end) - xScale(d.start);
})
.attr("height", function (d) {
return barScale(d.height);
})
.style("fill", function (d) {
return colorScale(d.height);
})
});
coverageFeature.move(function (el) {
var xScale = coverageFeature.scale();
el.select("g")
.select("rect")
.attr("x", function (d) {
return xScale(d.start);
})
.attr("width", function (d) {
return xScale(d.end) - xScale(d.start);
})
});
function getHeightInStep(arr) {
// mean of the data in the subarray passed as argument
return d3.sum(arr, function (d) {
return d.height;
}) / arr.length;
}
function getRangedData(data, to, from, steps) {
var stepLength = (to - from) / steps;
var slice = [];
for (var i = from; i < to; i += stepLength) {
slice.push({
start: i,
end: (i + stepLength),
height: getHeightInStep(data.slice(i, (i + stepLength)))
});
}
return slice;
}
// The board
var myBoard = tnt.board()
.from(0)
.to(1000)
.max(1000)
.zoom_in(50)
.zoom_out(1000);
// The location track
var location_track = tnt.board.track()
.height(20)
.color("white")
.display(tnt.board.track.feature.axis()
.orientation("top")
);
// The ranges track
var ranges_track = tnt.board.track()
.label("coverage plot")
.height(80)
.color("white")
.data (tnt.board.track.data.sync()
.retriever (function (loc) {
// Return only the range on display
// Keep a constant same number of steps (bars) on view
return getRangedData(data, loc.to, loc.from, 50);
})
)
.display(coverageFeature);
// Add the tracks and start
myBoard
.add_track(location_track)
.add_track(ranges_track);
myBoard;
')
Session Info
sessionInfo()
Marlin-Na/TnT documentation built on Sept. 15, 2024, 5:27 a.m.
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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"))
Coverage Feature
https://github.com/tntvis/tnt.board/blob/master/examples/dynamic_ranges/ranges.js
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// The coverage custom feature var coverageFeature = tnt.board.track.feature() .index(function(d) { return d.start + "-" + d.end; }); var coverageFeatureInverse = tnt.board.track.feature() .index(function(d) { return d.start + "-" + d.end; }); // Create new elements coverageFeature.create(function (el) { var xScale = coverageFeature.scale(); var track = this; var y = track.height(); var barScale = d3.scale.linear() .domain([0, 1]) .range([0, y]); var colorScale = d3.scale.linear() .domain([0, 1]) .range(["#5ba633", "#027be3"]); var g = el .append("g"); g.append("rect") .attr("x", function (d) { return xScale(d.start); }) .attr("y", function (d) { return y - barScale(d.height); //return 0; }) .attr("width", function (d) { return xScale(d.end) - xScale(d.start); }) .attr("height", function (d) { return barScale(d.height); }) .style("fill", function (d) { return colorScale(d.height); }) }); coverageFeatureInverse.create(function (el) { var xScale = coverageFeature.scale(); var track = this; var y = track.height(); var barScale = d3.scale.linear() .domain([0, 1]) .range([0, y]); var colorScale = d3.scale.linear() .domain([0, 1]) .range(["#5ba633", "#027be3"]); var g = el .append("g"); g.append("rect") .attr("x", function (d) { return xScale(d.start); }) .attr("y", function (d) { //return y - barScale(d.height); return 0; }) .attr("width", function (d) { return xScale(d.end) - xScale(d.start); }) .attr("height", function (d) { return barScale(d.height); }) .style("fill", function (d) { return colorScale(d.height); }) }); coverageFeature.move(function (el) { var xScale = coverageFeature.scale(); el.select("g") .select("rect") .attr("x", function (d) { return xScale(d.start); }) .attr("width", function (d) { return xScale(d.end) - xScale(d.start); }) }); coverageFeatureInverse.move(function (el) { var xScale = coverageFeature.scale(); el.select("g") .select("rect") .attr("x", function (d) { return xScale(d.start); }) .attr("width", function (d) { return xScale(d.end) - xScale(d.start); }) }); // The board var myBoard = tnt.board().from(20).to(500).max(1000); // The location track var location_track = tnt.board.track() .height(20) .color("white") .display(tnt.board.track.feature.axis() .orientation("top") ); // The ranges track var ranges_track = tnt.board.track() .label("coverage plot") .height(80) .color("white") .data (tnt.board.track.data.sync() .retriever (function (loc) { // Return only the range on display var rangeData = data.filter(function (d) { return (d.start > loc.from) && (d.end < loc.to); }); // if necessary group or edit the number of elements to show // rangeData = getNewRange(data, loc) return rangeData; }) ) .display(coverageFeature); var ranges_track2 = tnt.board.track() .label("coverage plot") .height(80) .color("white") .data (tnt.board.track.data.sync() .retriever (function (loc) { // Return only the range on display var rangeData = data.filter(function (d) { return (d.start > loc.from) && (d.end < loc.to); }); // if necessary group or edit the number of elements to show // rangeData = getNewRange(data, loc) return rangeData; }) ) .display(coverageFeatureInverse); // Add the tracks and start myBoard .add_track(location_track) .add_track(ranges_track2) .add_track(ranges_track); myBoard //myBoard(document.getElementById("mydiv")); //myBoard.start(); ')
2
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0.154711}, {start: 997, end: 997, height: 0.673648}, {start: 998, end: 998, height: 0.323852}, {start: 999, end: 999, height: 0.347196}, {start: 1000, end: 1000, height: 0.532514} ]; // The coverage custom feature var coverageFeature = tnt.board.track.feature() .index(function(d) { return d.start + "-" + d.end; }); // Create new elements coverageFeature.create(function (el) { var xScale = coverageFeature.scale(); var track = this; var y = track.height(); var barScale = d3.scale.linear() .domain([0, 1]) .range([0, y]); var colorScale = d3.scale.linear() .domain([0, 1]) .range(["#5ba633", "#027be3"]); var g = el .append("g"); g.append("rect") .attr("x", function (d) { return xScale(d.start); }) .attr("y", function (d) { return y - barScale(d.height); }) .attr("width", function (d) { return xScale(d.end) - xScale(d.start); }) .attr("height", function (d) { return barScale(d.height); }) .style("fill", function (d) { return colorScale(d.height); }) }); coverageFeature.move(function (el) { var xScale = coverageFeature.scale(); el.select("g") .select("rect") .attr("x", function (d) { return xScale(d.start); }) .attr("width", function (d) { return xScale(d.end) - xScale(d.start); }) }); function getHeightInStep(arr) { // mean of the data in the subarray passed as argument return d3.sum(arr, function (d) { return d.height; }) / arr.length; } function getRangedData(data, to, from, steps) { var stepLength = (to - from) / steps; var slice = []; for (var i = from; i < to; i += stepLength) { slice.push({ start: i, end: (i + stepLength), height: getHeightInStep(data.slice(i, (i + stepLength))) }); } return slice; } // The board var myBoard = tnt.board() .from(0) .to(1000) .max(1000) .zoom_in(50) .zoom_out(1000); // The location track var location_track = tnt.board.track() .height(20) .color("white") .display(tnt.board.track.feature.axis() .orientation("top") ); // The ranges track var ranges_track = tnt.board.track() .label("coverage plot") .height(80) .color("white") .data (tnt.board.track.data.sync() .retriever (function (loc) { // Return only the range on display // Keep a constant same number of steps (bars) on view return getRangedData(data, loc.to, loc.from, 50); }) ) .display(coverageFeature); // Add the tracks and start myBoard .add_track(location_track) .add_track(ranges_track); myBoard; ')
Session Info
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