Sandbox::https://github.com/MG-RAST/MG-RASTv4/blob/master/mg-rast.krona.html

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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">

<head>

{//-----------------------------------------------------------------------------

// PURPOSE

// Krona is a flexible tool for exploring the relative proportions of

// hierarchical data, such as metagenomic classifications, using a

// radial, space-filling display. It is implemented using HTML5 and

// JavaScript, allowing charts to be explored locally or served over the

// Internet, requiring only a current version of any major web

// browser. Krona charts can be created using an Excel template or from

// common bioinformatic formats using the provided conversion scripts.

// COPYRIGHT LICENSE

// Adam Phillippy

// This Software was prepared for the Department of Homeland Security

// (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as

// part of contract HSHQDC-07-C-00020 to manage and operate the National

// Biodefense Analysis and Countermeasures Center (NBACC), a Federally

// Funded Research and Development Center.

// Redistribution and use in source and binary forms, with or without

// modification, are permitted provided that the following conditions are

// met:

// * Redistributions of source code must retain the above copyright

// notice, this list of conditions and the following disclaimer.

// * Redistributions in binary form must reproduce the above copyright

// notice, this list of conditions and the following disclaimer in the

// documentation and/or other materials provided with the distribution.

// * Neither the name of the Battelle National Biodefense Institute nor

// the names of its contributors may be used to endorse or promote

// products derived from this software without specific prior written

// permission.

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

// HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

// TRADEMARK LICENSE

// KRONA(TM) is a trademark of the Department of Homeland Security, and use

// of the trademark is subject to the following conditions:

// * Distribution of the unchanged, official code/software using the

// KRONA(TM) mark is hereby permitted by the Department of Homeland

// Security, provided that the software is distributed without charge

// and modification.

// * Distribution of altered source code/software using the KRONA(TM) mark

// is not permitted unless written permission has been granted by the

// Department of Homeland Security.

// FOR MORE INFORMATION VISIT

// https://github.com/marbl/Krona/wiki/

//-----------------------------------------------------------------------------

}

var canvas;

var context;

var svg; // for snapshot mode

var collapse = true;

var collapseCheckBox;

var collapseLast;

var compress;

var compressCheckBox;

var maxAbsoluteDepthText;

var maxAbsoluteDepthButtonDecrease;

var maxAbsoluteDepthButtonIncrease;

var fontSize = 11;

var fontSizeText;

var fontSizeButtonDecrease;

var fontSizeButtonIncrease;

var fontSizeLast;

var radiusButtonDecrease;

var radiusButtonIncrease;

var shorten;

var shortenCheckBox;

var maxAbsoluteDepth;

var backButton;

var upButton;

var forwardButton;

var snapshotButton;

var snapshotMode = false;

var details;

var detailsName;

var search;

var searchResults;

var nSearchResults;

var useHueCheckBox;

var useHueDiv;

var datasetDropDown;

var datasetButtonLast;

var datasetButtonPrev;

var datasetButtonNext;

var keyControl;

var showKeys = true;

var linkButton;

var linkText;

var frame;

// Node references. Note that the meanings of 'selected' and 'focused' are

// swapped in the docs.

var head; // the root of the entire tree

var selectedNode = 0; // the root of the current view

var focusNode = 0; // a node chosen for more info (single-click)

var highlightedNode = 0; // mouse hover node

var highlightingHidden = false;

var nodes = new Array();

var currentNodeID = 0; // to iterate while loading

var nodeHistory = new Array();

var nodeHistoryPosition = 0;

var dataEnabled = false; // true when supplemental files are present

// store non-Krona GET variables so they can be passed on to links

var getVariables = new Array();

// selectedNodeLast is separate from the history, since we need to check

// properties of the last node viewed when browsing through the history

var selectedNodeLast = 0;

var zoomOut = false;

// temporary zoom-in while holding the mouse button on a wedge

var quickLook = false; // true when in quick look state

var mouseDown = false;

var mouseDownTime; // to detect mouse button hold

var quickLookHoldLength = 200;

var imageWidth;

var imageHeight;

var centerX;

var centerY;

var gRadius;

var updateViewNeeded = false;

// Determines the angle that the pie chart starts at. 90 degrees makes the

// center label consistent with the children.

var rotationOffset = Math.PI / 2;

var buffer;

var bufferFactor = .1;

// The maps are the small pie charts showing the current slice being viewed.

var mapBuffer = 10;

var mapRadius = 0;

var maxMapRadius = 25;

var mapWidth = 150;

var maxLabelOverhang = Math.PI * 4.18;

// Keys are the labeled boxes for slices in the highest level that are too thin

// to label.

var maxKeySizeFactor = 2; // will be multiplied by font size

var keySize;

var keys;

var keyBuffer = 10;

var currentKey;

var keyMinTextLeft;

var keyMinAngle;

var minRingWidthFactor = 5; // will be multiplied by font size

var maxPossibleDepth; // the theoretical max that can be displayed

var maxDisplayDepth; // the actual depth that will be displayed

var headerHeight = 0;//document.getElementById('options').clientHeight;

var historySpacingFactor = 1.6; // will be multiplied by font size

var historyAlphaDelta = .25;

// appearance

var lineOpacity = 0.3;

var saturation = 0.5;

var lightnessBase = 0.6;

var lightnessMax = .8;

var thinLineWidth = .3;

var highlightLineWidth = 1.5;

var labelBoxBuffer = 6;

var labelBoxRounding = 15;

var labelWidthFudge = 1.05; // The width of unshortened labels are set slightly

// longer than the name width so the animation

// finishes faster.

var fontNormal;

var fontBold;

var fontFamily = 'sans-serif';

//var fontFaceBold = 'bold Arial';

var nodeRadius;

var angleFactor;

var tickLength;

var compressedRadii;

// colors

var highlightFill = 'rgba(255, 255, 255, .3)';

var colorUnclassified = 'rgb(220,220,220)';

// label staggering

var labelOffsets; // will store the current offset at each depth

// This will store pointers to the last node that had a label in each offset (or "track") of a

// each depth. These will be used to shorten neighboring labels that would overlap.

// The [nLabelNodes] index will store the last node with a radial label.

// labelFirstNodes is the same, but to check for going all the way around and

// overlapping the first labels.

var labelLastNodes;

var labelFirstNodes;

var nLabelOffsets = 3; // the number of offsets to use

var mouseX = -1;

var mouseY = -1;

var mouseXRel = -1;

var mouseYRel = -1;

// tweening

var progress = 0; // for tweening; goes from 0 to 1.

var progressLast = 0;

var tweenFactor = 0; // progress converted by a curve for a smoother effect.

var tweenLength = 850; // in ms

var tweenCurvature = 13;

// tweenMax is used to scale the sigmoid function so its range is [0,1] for the

// domain [0,1]

var tweenMax = 1 / (1 + Math.exp(-tweenCurvature / 2));

var tweenStartTime;

// for framerate debug

var tweenFrames = 0;

var fpsDisplay = document.getElementById('frameRate');

// Arrays to translate xml attribute names into displayable attribute names

var attributes = new Array();

var magnitudeIndex; // the index of attribute arrays used for magnitude

var membersAssignedIndex;

var membersSummaryIndex;

// For defining gradients

var hueDisplayName;

var hueStopPositions;

var hueStopHues;

var hueStopText;

// multiple datasets

var currentDataset = 0;

var lastDataset = 0;

var datasets = 1;

var datasetNames;

var datasetSelectSize = 30;

var datasetAlpha = new Tween(0, 0);

var datasetWidths = new Array();

var datasetChanged;

var datasetSelectWidth = 50;

var image;

var hiddenPattern;

var loadingImage;

var logoImage;

function backingScale()

{

if ('devicePixelRatio' in window)

{

if (window.devicePixelRatio > 1)

{

return window.devicePixelRatio;

}

return 1;

}

function resize()

{

imageWidth = window.innerWidth;

imageHeight = window.innerHeight;

if ( ! snapshotMode )

{

context.canvas.width = imageWidth * backingScale();

context.canvas.height = imageHeight * backingScale();

context.canvas.style.width = imageWidth + "px"

context.canvas.style.height = imageHeight + "px"

context.scale(backingScale(), backingScale());

}

if ( datasetDropDown )

{

var ratio =

(datasetDropDown.offsetTop + datasetDropDown.clientHeight) * 2 /

imageHeight;

if ( ratio > 1 )

{

ratio = 1;

}

ratio = Math.sqrt(ratio);

datasetSelectWidth =

(datasetDropDown.offsetLeft + datasetDropDown.clientWidth) * ratio;

}

var leftMargin = datasets > 1 ? datasetSelectWidth + 30 : 0;

var minDimension = imageWidth - mapWidth - leftMargin > imageHeight ?

imageHeight :

imageWidth - mapWidth - leftMargin;

maxMapRadius = minDimension * .03;

buffer = minDimension * bufferFactor;

margin = minDimension * .015;

centerX = (imageWidth - mapWidth - leftMargin) / 2 + leftMargin;

centerY = imageHeight / 2;

gRadius = minDimension / 2 - buffer;

//context.font = '11px sans-serif';

}

function handleResize()

{

updateViewNeeded = true;

}

function Attribute()

{

}

function Tween(start, end)

{

this.start = start;

this.end = end;

this.current = this.start;

this.current = function()

{

if ( progress == 1 || this.start == this.end )

{

return this.end;

}

else

{

return this.start + tweenFactor * (this.end - this.start);

}

};

this.setTarget = function(target)

{

this.start = this.current();

this.end = target;

}

function Node()

{

this.id = currentNodeID;

currentNodeID++;

nodes[this.id] = this;

this.angleStart = new Tween(Math.PI, 0);

this.angleEnd = new Tween(Math.PI, 0);

this.radiusInner = new Tween(1, 1);

this.labelRadius = new Tween(1, 1);

this.labelWidth = new Tween(0, 0);

this.scale = new Tween(1, 1); // TEMP

this.radiusOuter = new Tween(1, 1);

this.r = new Tween(255, 255);

this.g = new Tween(255, 255);

this.b = new Tween(255, 255);

this.alphaLabel = new Tween(0, 1);

this.alphaLine = new Tween(0, 1);

this.alphaArc = new Tween(0, 0);

this.alphaWedge = new Tween(0, 1);

this.alphaOther = new Tween(0, 1);

this.alphaPattern = new Tween(0, 0);

this.children = Array();

this.parent = 0;

this.attributes = new Array(attributes.length);

this.addChild = function(child)

{

this.children.push(child);

};

this.addLabelNode = function(depth, labelOffset)

{

if ( labelHeadNodes[depth][labelOffset] == 0 )

{

// this will become the head node for this list

labelHeadNodes[depth][labelOffset] = this;

this.labelPrev = this;

}

var head = labelHeadNodes[depth][labelOffset];

this.labelNext = head;

this.labelPrev = head.labelPrev;

head.labelPrev.labelNext = this;

head.labelPrev = this;

}

this.canDisplayDepth = function()

{

// whether this node is at a depth that can be displayed, according

// to the max absolute depth

return this.depth <= maxAbsoluteDepth;

}

this.canDisplayHistory = function()

{

var radiusInner;

if ( compress )

{

radiusInner = compressedRadii[0];

}

else

{

radiusInner = nodeRadius;

}

return (

-this.labelRadius.end * gRadius +

historySpacingFactor * fontSize / 2 <

radiusInner * gRadius

);

}

this.canDisplayLabelCurrent = function()

{

return (

(this.angleEnd.current() - this.angleStart.current()) *

(this.radiusInner.current() * gRadius + gRadius) >=

minWidth());

}

this.checkHighlight = function()

{

if ( this.children.length == 0 && this == focusNode )

{

//return false;

}

if ( this.hide )

{

return false;

}

if ( this.radiusInner.end == 1 )

{

// compressed to the outside; don't check

return false;

}

var highlighted = false;

var angleStartCurrent = this.angleStart.current() + rotationOffset;

var angleEndCurrent = this.angleEnd.current() + rotationOffset;

var radiusInner = this.radiusInner.current() * gRadius;

for ( var i = 0; i < this.children.length; i++ )

{

highlighted = this.children[i].checkHighlight();

if ( highlighted )

{

return true;

}

if ( this.radial )

{

var angleText = (angleStartCurrent + angleEndCurrent) / 2;

var radiusText = (gRadius + radiusInner) / 2;

context.rotate(angleText);

context.beginPath();

context.moveTo(radiusText, -fontSize);

context.lineTo(radiusText, fontSize);

context.lineTo(radiusText + centerX, fontSize);

context.lineTo(radiusText + centerX, -fontSize);

context.closePath();

context.rotate(-angleText);

if ( context.isPointInPath(mouseXRel, mouseYRel) )

{

var label = String(this.getPercentage()) + '%' + ' ' + this.name;

if ( this.searchResultChildren() )

{

label += searchResultString(this.searchResultChildren());

}

(

Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() <

radiusText + measureText(label)

)

{

highlighted = true;

}

else

{

for ( var i = 0; i < this.hiddenLabels.length; i++ )

{

var hiddenLabel = this.hiddenLabels[i];

context.rotate(hiddenLabel.angle);

context.beginPath();

context.moveTo(gRadius, -fontSize);

context.lineTo(gRadius, fontSize);

context.lineTo(gRadius + centerX, fontSize);

context.lineTo(gRadius + centerX, -fontSize);

context.closePath();

context.rotate(-hiddenLabel.angle);

if ( context.isPointInPath(mouseXRel, mouseYRel) )

{

var label = String(hiddenLabel.value) + ' more';

if ( hiddenLabel.search )

{

label += searchResultString(hiddenLabel.search);

}

(

Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() <

gRadius + fontSize + measureText(label)

)

{

highlighted = true;

break;

}

if ( ! highlighted && this != selectedNode && ! this.getCollapse() )

{

context.beginPath();

context.arc(0, 0, radiusInner, angleStartCurrent, angleEndCurrent, false);

context.arc(0, 0, gRadius, angleEndCurrent, angleStartCurrent, true);

context.closePath();

if ( context.isPointInPath(mouseXRel, mouseYRel) )

{

highlighted = true;

}

(

! highlighted &&

(angleEndCurrent - angleStartCurrent) *

(radiusInner + gRadius) <

minWidth() &&

this.getDepth() == selectedNode.getDepth() + 1

)

{

if ( showKeys && this.checkHighlightKey() )

{

highlighted = true;

}

if ( highlighted )

{

if ( this != highlightedNode )

{

// document.body.style.cursor='pointer';

}

highlightedNode = this;

}

return highlighted;

}

this.checkHighlightCenter = function()

{

if ( ! this.canDisplayHistory() )

{

return;

}

var cx = centerX;

var cy = centerY - this.labelRadius.end * gRadius;

//var dim = context.measureText(this.name);

var width = this.nameWidth;

if ( this.searchResultChildren() )

{

var results = searchResultString(this.searchResultChildren());

var dim = context.measureText(results);

width += dim.width;

}

(

mouseX > cx - width / 2 &&

mouseX < cx + width / 2 &&

mouseY > cy - historySpacingFactor * fontSize / 2 &&

mouseY < cy + historySpacingFactor * fontSize / 2

)

{

highlightedNode = this;

return;

}

if ( this.getParent() )

{

this.getParent().checkHighlightCenter();

}

this.checkHighlightKey = function()

{

var offset = keyOffset();

var xMin = imageWidth - keySize - margin - this.keyNameWidth - keyBuffer;

var xMax = imageWidth - margin;

var yMin = offset;

var yMax = offset + keySize;

currentKey++;

return (

mouseX > xMin &&

mouseX < xMax &&

mouseY > yMin &&

mouseY < yMax);

}

this.checkHighlightMap = function()

{

if ( this.parent )

{

this.parent.checkHighlightMap();

}

if ( this.getCollapse() || this == focusNode )

{

return;

}

var box = this.getMapPosition();

(

mouseX > box.x - mapRadius &&

mouseX < box.x + mapRadius &&

mouseY > box.y - mapRadius &&

mouseY < box.y + mapRadius

)

{

highlightedNode = this;

}

/* this.collapse = function()

{

for (var i = 0; i < this.children.length; i++ )

{

this.children[i] = this.children[i].collapse();

}

(

this.children.length == 1 &&

this.children[0].magnitude == this.magnitude

)

{

this.children[0].parent = this.parent;

this.children[0].getDepth() = this.parent.getDepth() + 1;

return this.children[0];

}

else

{

return this;

}

this.draw = function(labelMode, selected, searchHighlighted)

{

var depth = this.getDepth() - selectedNode.getDepth() + 1;

// var hidden = false;

if ( selectedNode == this )

{

selected = true;

}

var angleStartCurrent = this.angleStart.current() + rotationOffset;

var angleEndCurrent = this.angleEnd.current() + rotationOffset;

var radiusInner = this.radiusInner.current() * gRadius;

var canDisplayLabelCurrent = this.canDisplayLabelCurrent();

var hiddenSearchResults = false;

/* if ( ! this.hide )

{

for ( var i = 0; i < this.children.length; i++ )

{

if ( this.children[i].hide && this.children[i].searchResults )

{

hiddenSearchResults = true;

}

var drawChildren =

( ! this.hide || ! this.hidePrev && progress < 1 ) &&

( ! this.hideAlone || ! this.hideAlonePrev && progress < 1 );

// if ( this.alphaWedge.current() > 0 || this.alphaLabel.current() > 0 )

{

var lastChildAngleEnd;

if ( this.hasChildren() )//canDisplayChildren )

{

lastChildAngleEnd =

this.children[this.children.length - 1].angleEnd.current()

+ rotationOffset;

}

if ( labelMode )

{

var drawRadial =

this.parent &&

this.parent != selectedNode &&

angleEndCurrent == this.parent.angleEnd.current() + rotationOffset

);

if ( angleStartCurrent != angleEndCurrent )

{

this.drawLines(angleStartCurrent, angleEndCurrent, radiusInner, drawRadial, selected);

}

var alphaOtherCurrent = this.alphaOther.current();

var childRadiusInner;

if ( this == selectedNode || alphaOtherCurrent )

{

childRadiusInner =

this.children[this.children.length - 1].radiusInner.current() * gRadius;

}

if ( this == selectedNode )

{

this.drawReferenceRings(childRadiusInner);

}

(

selected &&

! searchHighlighted &&

this != selectedNode &&

(

this.isSearchResult ||

this.hideAlone && this.searchResultChildren() ||

false

// this.hide &&

// this.containsSearchResult

)

{

context.globalAlpha = this.alphaWedge.current();

drawWedge

(

angleStartCurrent,

angleEndCurrent,

radiusInner,

gRadius,

highlightFill,

true

);

(

this.keyed &&

! showKeys &&

this.searchResults &&

! searchHighlighted &&

this != highlightedNode &&

this != focusNode

)

{

var angle = (angleEndCurrent + angleStartCurrent) / 2;

this.drawLabel(angle, true, false, true, true);

}

//this.drawHighlight(false);

searchHighlighted = true;

}

(

this == selectedNode ||

// true

//(canDisplayLabelCurrent) &&

this != highlightedNode &&

this != focusNode

)

{

if ( this.radial != this.radialPrev && this.alphaLabel.end == 1 )

{

context.globalAlpha = tweenFactor;

}

else

{

context.globalAlpha = this.alphaLabel.current();

}

this.drawLabel

(

(angleStartCurrent + angleEndCurrent) / 2,

this.hideAlone && this.searchResultChildren() ||

(this.isSearchResult || hiddenSearchResults) && selected,

this == selectedNode && ! this.radial,

selected,

this.radial

);

if ( this.radial != this.radialPrev && this.alphaLabel.start == 1 && progress < 1 )

{

context.globalAlpha = 1 - tweenFactor;

this.drawLabel

(

(angleStartCurrent + angleEndCurrent) / 2,

(this.isSearchResult || hiddenSearchResults) && selected,

this == selectedNodeLast && ! this.radialPrev,

selected,

this.radialPrev

);

}

(

alphaOtherCurrent &&

lastChildAngleEnd != null

)

{

(

(angleEndCurrent - lastChildAngleEnd) *

(childRadiusInner + gRadius) >=

minWidth()

)

{

//context.font = fontNormal;

context.globalAlpha = this.alphaOther.current();

drawTextPolar

(

this.getUnclassifiedText(),

this.getUnclassifiedPercentage(),

(lastChildAngleEnd + angleEndCurrent) / 2,

(childRadiusInner + gRadius) / 2,

true,

false,

);

}

if ( this == selectedNode && this.keyUnclassified && showKeys )

{

this.drawKey

(

(lastChildAngleEnd + angleEndCurrent) / 2,

false,

false

);

}

else

{

var alphaWedgeCurrent = this.alphaWedge.current();

if ( alphaWedgeCurrent || this.alphaOther.current() )

{

var currentR = this.r.current();

var currentG = this.g.current();

var currentB = this.b.current();

var fill = rgbText(currentR, currentG, currentB);

var radiusOuter;

var lastChildAngle;

var truncateWedge =

(

this.hasChildren() &&

! this.keyed &&

(compress || depth < maxDisplayDepth) &&

drawChildren

);

if ( truncateWedge )

{

radiusOuter = this.children[0].radiusInner.current() * gRadius;

}

else

{

radiusOuter = gRadius;

}

if ( this.hasChildren() )

{

radiusOuter = this.children[0].getUncollapsed().radiusInner.current() * gRadius + 1;

}

else

{ // TEMP

radiusOuter = radiusInner + nodeRadius * gRadius;

if ( radiusOuter > gRadius )

{

radiusOuter = gRadius;

}

context.globalAlpha = alphaWedgeCurrent;

if ( radiusInner != radiusOuter )

{

drawWedge

(

angleStartCurrent,

angleEndCurrent,

radiusInner,

radiusOuter,//this.radiusOuter.current() * gRadius,

//'rgba(0, 200, 0, .1)',

fill,

this.alphaPattern.current()

);

if ( truncateWedge )

{

// fill in the extra space if the sum of our childrens'

// magnitudes is less than ours

if ( lastChildAngleEnd < angleEndCurrent )//&& false) // TEMP

{

if ( radiusOuter > 1 )

{

// overlap slightly to hide the seam

// radiusOuter -= 1;

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