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jsproteinmapper.js
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jsproteinmapper.js
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jsProteinMapper = function(){
var _this = this;
var default_opts={
target:'body',
pfamData:null, //response from pfam proxy
variantOfInterest:{},//{codon, annotation[{lable,text},... ] }
variantTracks:[],//array of objects with properties "label" as name of variant set, and "data" as array of objects with properties "codon", "pdot" and "cdna"
width:775,
height:300,
fontSize:16,
variantColor:'red',
lollipopHeight:15,
lollipopHeadSize:6,
disulphideBridgeHeightIncrement:0,
regionHeight:16,
sequenceHeight:7,
tracksYOffset:20,
padding:25,
trackFillColor:'none',
showControls:true,
tooltip:'hover',
};
var container,
proteinlabelcontainer,
s,
loading,
xscale,
trackscale,
opts,
tracks,
zoom_graphic,
w,
h,
lollipopHeight,
lollipopHeadSize,
regionHeight,
sequenceHeight,
tracksYOffset,
scaleExtentX = 10,
scaleExtentY,
zoomToSelection=false;
xscale = d3.scaleLinear();
xscale.scalefactor=1;//use this field to implement cross-element scale clamping
trackscale = d3.scaleBand();
xaxis_bottom = d3.axisBottom(xscale);
xaxis_top=d3.axisTop(xscale);
tooltip = d3.tip()
.attr('class', 'd3-tip')
.offset([-10, 0])
.html(function (d) {
var div = $('<div>');
tooltip.element=div;
var m = d.tooltip;
if (!m) {
return null;
}
if(m instanceof jQuery) div.append(m.clone());
else div.append(m);
div.append($('<div>',{class:'tooltip-close'}) )
return div.html();
})
.direction(function(d){
//var h = tooltip.html();
return 'n';
});
$('body').on('click','.tooltip-close',tooltip.hide );
zoom_graphic = d3.zoom()
.on('zoom', dispatchZoom);
_this.init = function(options){
//Read in options structure and merge with defaults
opts = $.extend({},default_opts,options);
//copy values to "local" variables for ease of use
w = opts.width;
h = opts.height;
lollipopHeight=opts.lollipopHeight;
lollipopHeadSize=opts.lollipopHeadSize;
regionHeight=opts.regionHeight;
sequenceHeight=opts.sequenceHeight;
padding=opts.padding,
tracksYOffset=opts.tracksYOffset;
//set the range of the xscale object
xscale.range([0,w]);
//clear old widget if needed
d3.select(opts.target).select('.jsproteinmapper').remove();
//create new widget
var widgetcontainer=$('<div>',{class:'jsproteinmapper'}).appendTo(opts.target);
container = $('<div>',{class:'svgcontainer'}).css({width:w,height:h});
//setup "loading" overlay
loading=$('<div>',{class:'loading-overlay'}).text('Waiting for data...').appendTo(container);
//append widget to target element
container.appendTo(widgetcontainer);
proteinlabelcontainer = $('<div>',{class:'proteinlabelcontainer'}).appendTo(widgetcontainer);
//create svg element; store reference as variable "s"
s = d3.select(container.get(0))
.append('svg')
.attr('style','box-sizing:border-box; overflow:visible;')
.attr('width',w)
.attr('height',h)
.attr('viewBox','-'+padding+',-'+padding+','+(w+2*padding)+','+(h+2*padding) )
.call(tooltip);
//Register event handlers to handle zoom/pan behavior
//Custom handlers first; then selection.call(zoom) to register those handlers later
//mousedown.zoomToSelection event needed to start zoom-to-rectangle behavior
s.on('mousedown.zoomToSelection',dispatchZoom, true);
//now add zoom handlers
s.call(zoom_graphic);
//disable text selection to not interfere with zoom/drag behavior
s.style('-webkit-touch-callout','none')
.style('-webkit-user-select','none')
.style('-khtml-user-select','none')
.style('-moz-user-select','none')
.style('-ms-user-select','none')
.style('user-select','none');
//Add methods to the public API of the widget
_this.drawWidget = function(options){
s.selectAll("*").remove();//clear svg element first
drawProteinStructure();
drawVariant();
drawVariantTracks();
loading.hide();
};
//If these data are not available on initialization of the widget, they can be set later. Returns reference to widget for method chaining.
_this.setPfamData=function(pfamData){
opts.pfamData=pfamData;
return _this;
}
_this.setVariant = function(variant){
opts.variantOfInterest=variant;
return _this;
}
_this.setTracks = function(track_array){
opts.variantTracks = track_array;
return _this;
}
//return reference to the widget
return _this;
}
//Helper functions for some default implementations of data handling
//function defs below.
_this.helpers={
pfamAjaxResults: pfamAjaxResults,
parseVariantString: parseVariantString,
aggregate:aggregate,
tooltips:{
basicTooltip:makeBasicTooltip,
variantTable:variantTable,
variantPiechart:variantPiechart,
variantBarchart:variantBarchart,
},
}
return _this;
//Internal methods
function drawProteinStructure(){
var r = opts.pfamData;
var seq_len = Number(r.length);
scaleExtentX = seq_len/20;
xscale.domain([0, seq_len]);
xaxis_bottom.scale(xscale);
xaxis_top.scale(xscale);
s.append('g').attr('transform','translate(0,'+h+')').attr('class','xaxis bottom').call(xaxis_bottom);
toNumber(r);
setHeights(r.markups,lollipopHeight,lollipopHeadSize,xscale);
var identifier = r.metadata.identifier;
var m =identifier.match(/([^_]*).*/i);
if(m && m.length>1) identifier = m[1]; //strip trailing _HUMAN or other underscore-separated text from the identifier
identifier += ' (' + r.metadata.accession + ':'+r.metadata.database+')';
proteinlabelcontainer.text(identifier);
var seqc = s.append('g')
.attr('class','sequence-container')
.attr('transform','translate(0,'+(h-(lollipopHeight+lollipopHeadSize))+')');
var seq = seqc.append('g').attr('class','sequence');
seq.selectAll('.sequence-base')
.data([{length:r.length,height:opts.sequenceHeight}])
.enter()
.append('rect')
.attr('width',function(d){
return xscale(d.length)-xscale(0); })
.attr('height',function(d){
return d.height})
.attr('fill','gray')
.attr('y',function(d){return -1*(d.height/2)})
.attr('x',xscale(0));
seq.append('g').attr('class','pfam-regions')
.selectAll('.pfam-region')
.data(r.regions)
.enter()
.append('path')
.attr('class','pfam-region has-tooltip')
.attr('d',function(d){return PfamRegion(d);})
.attr('fill',function(d){return d.colour;})
.on('mouseover',tooltip.show)
.on('mouseout',tooltip.hide);
seqc.append('g').attr('class','pfam-annotations')
.selectAll('.pfam-annotation')
.data(r.markups)
.enter()
.append(function(d){return makeAnnotation(d); });
}
function drawVariant(){
var d = opts.variantOfInterest;
if(!d.codon) return;
var info=Object.assign({},{title:'Variant of interest',Codon:d.codon}, d.annotation);
d.tooltip = makeBasicTooltip(info);
s.selectAll('.variant')
.data([d])
.enter()
.append('rect')
.attr('class','variant has-tooltip')
.attr('y',0)
.attr('height',h)
.attr('x',function(d){ return xscale(d.codon-0.5); })
.attr('width',function(d){ return Math.max(xscale(1)-xscale(0), 1); })
.attr('fill',opts.variantColor)
.attr('stroke','none')
.on('mouseover',tooltip.show)
.on('mouseout',tooltip.hide);
}
function drawVariantTracks(){
tracks = opts.variantTracks;
var numTracks = tracks.length;
if (numTracks==0) return;
s.append('g').attr('class','xaxis top').call(xaxis_top);
var tracks_y = h - (lollipopHeight*2+lollipopHeadSize*2+tracksYOffset);
d3.select('.zoom-x').attr('height',h-tracks_y).attr('y',-1*(tracksYOffset+lollipopHeight+lollipopHeadSize));
trackscale.domain(tracks.map(function(e,i){ return e.label; }) )
.range([0, tracks_y])
.paddingInner(0.1);
for(var i=0;i<numTracks;++i){
tracks[i].yscalelinear=d3.scaleLinear().range([trackscale.bandwidth(),0]).domain([0,d3.max(tracks[i].data,function(d){return d.count; })*1.1 ]);
tracks[i].yscalelog=d3.scaleLog().range([trackscale.bandwidth(),0.1]).domain([0.1,d3.max(tracks[i].data,function(d){return d.count; })*1.5 ]);
tracks[i].yscale=tracks[i].yscalelinear.copy();
tracks[i].yaxis=d3.axisLeft(tracks[i].yscale).ticks(5,'.0s')
.tickFormat((v,i,a)=>{
if(Math.floor(v)!==v || v<1) return;
if(a.length>10){
var pow= Math.log10(v);
//console.log(v,pow,Math.floor(pow));
if(i!==a.length-1 && Math.floor(pow) !== pow) return;
}
return v;
});
}
var tracks_container = s.append('g')
.attr('class','tracks-container');
tracks_container
.selectAll('.track')
.data(tracks)
.enter()
.append('g')
.attr('class','track')
.attr('transform',function(d){return 'translate(0,' + trackscale(d.label) +')'})
.append('svg') //add svg element to clip the graphs if the scaling or panning overflows
.attr('width',w)
.attr('height',trackscale.bandwidth())
.each(drawHistogram,xscale)
tracks_container.selectAll('.bar')
.on('mouseover',tooltip.show)
.on('mouseout',tooltip.hide);
//create background rectangles
var trackOpacity = 0.5
if(opts.trackFillColor == 'none'){
opts.trackFillColor = 'white';
trackOpacity = 0.0;
}
d3.selectAll('.track')
.append('rect')
.attr('width',w)
.attr('height',function(d){
return trackscale.bandwidth(); })
.attr('fill',opts.trackFillColor)
.attr('fill-opacity',trackOpacity)
.attr('stroke','gray')
.lower();
//add text labels
d3.selectAll('.track')
.append('text')
.attr('x',5)
.attr('y',5)
.attr('alignment-baseline','hanging')
.text(function(d){return d.label; });
//add y axes
d3.selectAll('.track')
.append('g')
.attr('class','yaxis').each(function(d){
d3.select(this).call(d.yaxis);
});
var zy = d3.zoom()
.on('zoom',zoomY2)
.filter(function(){
if(event.type=='dblclick' || event.type=='touchstart' || (event.type=='wheel'&&(event.shiftKey || event.metaKey)) ){
return true;
}
else{
var zoom_func = s.on(event.type+'.zoom');
zoom_func.call(s.node());
return false;
}
});
//Options dialog
var optionsWindow=$('<div>',{class:'options-window'}).hide().appendTo(container);
$('<div>',{class:'options-background'}).appendTo(optionsWindow)
.on('click',()=>optionsWindow.hide());
var optionsPanel=$('<div>',{class:'options-panel'}).appendTo(optionsWindow);
$('<div>',{class:'close-button'}).appendTo(optionsPanel).on('click',()=>optionsWindow.hide());
var optionsDialog=$('<div>',{class:'options-dialog'}).appendTo(optionsPanel);
//add control buttons
//options
var uc=tracks_container.append('foreignObject')
.attr('class','control-object')
.attr('width',1)
.attr('height',1)
.attr('transform','translate('+(w-1)+',0)')
.append('xhtml:div')
.attr('class','user-controls controls');
uc.append('button')
.attr('class','control-button')
.text('Options')
.on('click',()=>{
optionsWindow.show();
//$(d3.event.target).toggleClass('active');
//$(tracks_container.node()).find('.track-controls').toggle()
});
var controlOption=$('<div>',{class:'option-item'}).appendTo(optionsDialog);
$('<span>',{class:'option-text'}).text('Clickable control buttons?').appendTo(controlOption);
var showControls=$('<button>',{class:'control-button active'}).appendTo(controlOption)
.text('Show controls')
.on('click',(ev)=>{
$(ev.target).toggleClass('active');
$(tracks_container.node()).find('.track-controls').toggle()
});
var tooltipOption=$('<div>',{class:'option-item'}).appendTo(optionsDialog);
$('<span>',{class:'option-text'}).text('Show tooltip on: ').appendTo(tooltipOption);
var tooltipHover=$('<button>',{class:'control-button tooltip-hover active'}).appendTo(tooltipOption)
.text('Hover')
.on('click',()=>{
optionsDialog.find('.tooltip-click').removeClass('active')
optionsDialog.find('.tooltip-hover').addClass('active')
container.addClass('tooltip-hover')
.removeClass('tooltip-click')
d3.select(tooltip.node())
.classed('tooltip-hover',true)
.classed('tooltip-click',false)
d3.selectAll('.has-tooltip')
.on('mouseover',tooltip.show)
.on('mouseout',tooltip.hide)
.on('click',null)
});
var tooltipClick=$('<button>',{class:'control-button tooltip-click'}).appendTo(tooltipOption)
.text('Click')
.on('click',()=>{
optionsDialog.find('.tooltip-hover').removeClass('active')
optionsDialog.find('.tooltip-click').addClass('active')
container.addClass('tooltip-click')
.removeClass('tooltip-hover')
d3.select(tooltip.node())
.classed('tooltip-hover',false)
.classed('tooltip-click',true)
d3.selectAll('.has-tooltip')
.on('mouseover',null)
.on('mouseout',null)
.on('click',tooltip.show)
});
//track-specific controls
//zoom controls
var zc = tracks_container.selectAll('.track svg')
.append('foreignObject')
.attr('class','control-object')
.attr('width',1)
.attr('height',1)
.attr('transform','translate('+(w-1)+',0)')
.append('xhtml:div')
.attr('class','track-controls zoom-controls controls')
zc.append('button')
.attr('class','zoom-in control-button')
.text('+')
.on('click',()=>{
d3.select($(d3.event.target).closest('.track')[0]).call(zy.scaleBy, 1.5)
})
var mid=zc.append('div').attr('class','mid');
mid.append('button')
.attr('class','control-button')
.text('<')
.on('click',()=>{
s.call(zoom_graphic.scaleBy,1/1.5);
});
mid.append('button')
.attr('class','control-button')
.text('x')
.on('click',()=>{
s.call(zoom_graphic.transform,d3.zoomIdentity);
$(d3.event.target).closest('.track').find('.scale.active').click();
});
mid.append('button')
.attr('class','control-button')
.text('>')
.on('click',()=>{
s.call(zoom_graphic.scaleBy,1.5);
});
zc.append('button')
.attr('class','zoom-out control-button')
.text('-')
.on('click',()=>{
d3.select($(d3.event.target).closest('.track')[0]).call(zy.scaleBy, 1/1.5)
})
//axis controls
var ac = tracks_container.selectAll('.track')
.append('foreignObject')
.attr('class','control-object')
.attr('width',1)
.attr('height',1)
.attr('transform','rotate(-90)')
.append('xhtml:div')
.attr('class','track-controls axis-controls controls')
.style('width',Math.floor(trackscale.bandwidth())+'px');
ac.append('button')
.attr('class','scale scale-linear control-button active')
.text('linear')
.on('click',linearScale);
ac.append('button')
.attr('class','scale control-button scale-log')
.text('log')
.on('click',logScale);
//attach the zoom handler to the data
tracks.forEach(function(e){e.zoom = zy;});
//add zoom event handlers
d3.selectAll('.track')
.call(zy);
//Handle user options for controls and tooltip
if(opts.showControls==false) showControls.click();
if(opts.tooltip=='click') tooltipClick.click();
else tooltipHover.click();
}
function drawHistogram(track){
var yscale = track.yscale;
var width = Math.max(xscale(1)-xscale(0), 1);
d3.select(this)
.selectAll('.bar')
.data(track.data)
.enter()
.append('g')
.attr('class','bar bar-x has-tooltip')
.attr('transform',(d)=>'translate('+xscale(d.codon-0.5)+',0)')
.append('g')
.attr('transform','translate(0,'+yscale.range()[0]+')')
.append('g')
.attr('class','bar-scale-x')
.attr('transform','scale('+width+',1)')
.append('g')
.attr('class','bar-scale-y')
.attr('transform','scale(1,-1)')
.selectAll('.track-item')
.data((d)=>{
var data={
yscale:(val)=>yscale.range()[0]-yscale(Math.max(val,yscale.domain()[0])),
d:d
}
return [data];
})
.enter()
.append('g')
.attr('class','track-item')
.call(drawTrackItem)
}
function drawTrackItem(p){
p.each(function(d){
var g=d3.select(this);
g.selectAll('*').remove();
var draw = d.d.drawTrackItem ? d.d.drawTrackItem : defaultBar;
var y=d.yscale;
var data=d.d;
g.datum(data);
draw(g,d.yscale);
})
}
function defaultBar(g,y){
g.append('rect')
.attr('class','redraw')
.attr('height',(d)=>y(d.count))
.attr('width',1)
.attr('fill',(d)=>d.color?d.color:'black')
.datum((d)=>{d.redraw=redraw;return d;})
function redraw(el,y){
el.attr('height',(d)=>y(d.count))
}
}
function dispatchZoom(){
//Dispatch to different event handlers depending on context of event
//Modifier keys: shift, ctrl
//Wheel (no-modifier):X-xoom
//Mod-wheel on trackgroup: Y-zoom
//Dblclick on trackgroup: Y-zoom
//Dblclick on background/protein graphic: X-zoom
//Drag (no-mod): X-pan
//Mod-drag: Begin selection rectangle, and zoom depending on context. Initiated in other handler (above)
switch(d3.event.type){
case 'mousedown':
var evt = event ||d3.event;
if(evt.shiftKey || evt.metaKey){
evt.path = evt.path || [];
var trackgroup =evt.path.find(function(e){ return /\btrack\b/.test(e.classList); });
zoomToSelection={};
zoomToSelection.point1 = d3.mouse(s.node());
zoomToSelection.trackgroup=trackgroup;
if(trackgroup){
var tg=d3.select(trackgroup);
zoomToSelection.point1[1]=trackscale.bandwidth();
zoomToSelection.ylim=[0, trackscale.bandwidth()];
zoomToSelection.zoomrect = tg.append("rect").attr("class", "zoom-rect").attr('stroke','black').attr('fill-opacity',0.4).attr('fill','white');
}
else{
zoomToSelection.point1[1]=h;
zoomToSelection.zoomrect = s.append("rect").attr("class", "zoom-rect").attr('stroke','black').attr('fill-opacity',0.4).attr('fill','white');
}
d3.event.stopImmediatePropagation();
d3.select(window)
.on("mousemove.zoomToSelection", dispatchZoom, true)
.on("mouseup.zoomToSelection", dispatchZoom, true);
}
break;
case 'mousemove':
if(zoomToSelection){
if(zoomToSelection.trackgroup){
//Zoom in X and Y: limit the selection rect to the trackgroup only
var m = d3.mouse(zoomToSelection.trackgroup);
m[1] = Math.max(0, m[1]);
if(m[1] >= zoomToSelection.ylim[1]) m[1]=0;
}
else{
//Zooming in X only: make the selection rect the entire height of the svg element
var m = d3.mouse(s.node());
m[1] = 0;
}
m[0] = Math.max(0, Math.min(w, m[0]));
var point1 = zoomToSelection.point1;
zoomToSelection.zoomrect.attr("x", Math.min(point1[0], m[0]))
.attr("y", Math.min(point1[1], m[1]))
.attr("width", Math.abs(m[0] - point1[0]))
.attr("height", Math.abs(m[1] - point1[1]));
d3.event.stopImmediatePropagation();
}
break;
case 'mouseup':
if(zoomToSelection){
d3.select(window)
.on("mousemove.zoomToSelection",null)
.on("mouseup.zoomToSelection",null);
var point2 = d3.mouse(s.node());
var point1=zoomToSelection.point1;
if (point2[0] !== point1[0] ) {
var x1=Math.min(point1[0], point2[0]);
var x2=Math.max(point1[0],point2[0]);
if(zoomToSelection.trackgroup){
//zoom to Y range
var tg=d3.select(zoomToSelection.trackgroup);
var d =tg .datum(); //get trackgroup's data
var multiplier=zoomToSelection.ylim[1] / zoomToSelection.zoomrect.attr('height');
tg.transition().duration(300).call(d.zoom.scaleBy, multiplier );
}
//zoom to x range in all cases
//get the current zoom transform for the svg node
var zt = d3.zoomTransform(s.node());
s.transition()
.duration(300)
.call(zoom_graphic.transform,
d3.zoomIdentity
.scale( zt.k * w/(x2-x1) )
.translate( -zt.invertX(x1), 0) );
}
zoomToSelection.zoomrect.remove();
zoomToSelection=false;
d3.event.stopImmediatePropagation();
}
break;
case 'zoom':
zoomX();
break;
default:
zoomX();
}
}
function zoomX(){
transform = d3.event.transform;
if(!transform) transform = d3.zoomIdentity;
var newX = transform.rescaleX(xscale);
d3.select('.sequence').attr('transform', 'translate(' + transform.x + ',' + 0 + ') scale(' + transform.k + ',1)');
d3.selectAll('.annotation.disulphide').attr('transform', function(d){
return 'translate(' + newX(d.start) +',' + 0 + ') scale(' + transform.k + ',1)';
});
d3.selectAll('.annotation.lollipop').attr('transform', function(d){
return 'translate(' + newX(d.start) +',' + 0 + ')';
});
xaxis_bottom.scale(newX);
xaxis_top.scale(newX);
d3.selectAll('.xaxis.bottom').call(xaxis_bottom);
d3.selectAll('.xaxis.top').call(xaxis_top);
d3.selectAll('.variant')
.attr('x',function(d){ return newX(d.codon-0.5); })
.attr('width',function(d){ return Math.max(newX(1)-newX(0), 1); });
d3.selectAll('.bar-x')
.attr('transform',(d)=>{
return 'translate('+newX(d.codon-0.5)+',0)'
//return 'translate('+(newX(d.codon)-Math.max(newX(0.5)-newX(0), 0.5))+',0)'
}).select('.bar-scale-x')
.attr('transform',(d)=>{
return 'scale('+Math.max(newX(1)-newX(0), 1)+',1)';
});
// d3.selectAll('.bar')
// .attr('x',function(d){ return newX(d.codon)-Math.max(newX(0.5)-newX(0), 0.5); })
// .attr('width',function(d){
// return Math.max(1, newX(1)-newX(0)); });
}
function zoomY2(d){
drawY(this,d)
}
function drawY(track,d,opt){
var track=d3.select(track);
//var y = d.yscale;//.copy();
var y = d.yscale.copy();
var domain=d.yscale.domain();
if(d3.event.transform){
domain[1]=domain[1] / d3.event.transform.k;
}
else if(opt){
switch(opt){
case 'in':domain[1]*=2; break;
case 'out':domain[1]*=0.5;break;
case 'reset':track.call(d.zoom.transform, d3.zoomIdentity);break;
}
}
if(domain[1]<=1){
track.call(d.zoom.transform, d3.zoomIdentity);
return;
}
y.domain(domain);
var zoom_factor=d.yscale.domain()[1]/domain[1];
track.selectAll('.track-item .redraw')
.each(function(d){
d.redraw(d3.select(this),(c)=>y.range()[0]-y(Math.max(c,y.domain()[0])) )
})
d.yaxis.scale(y);
track.select('.yaxis').call(d.yaxis);
}
function logScale(d){
console.log('log');
var button=$(this);
button.addClass('active');
var track=button.closest('.track');
button.closest('.track-controls').find('.scale-linear').removeClass('active');
d.yscale = d.yscalelog;
drawY(track[0],d,'reset');
}
function linearScale(d){
console.log('linear');
var button=$(this);
button.addClass('active');
var track=button.closest('.track');
button.closest('.track-controls').find('.scale-log').removeClass('active');
d.yscale = d.yscalelinear;
drawY(track[0],d,'reset');
}
function makeAnnotation(e){
var lollipopHeight=opts.lollipopHeight,
lollipopHeadSize=opts.lollipopHeadSize;
var g = d3.select(document.createElementNS(d3.namespaces.svg, 'g'));
var ys = e.v_align=="bottom"? 1 : -1;
switch(e.type){
case 'disulphide':
console.log('disulphide');
var color=e.colour;
var lineColor=e.lineColour;
g.append('path')
.attr('d','M'+0+','+0+',v'+(e.height*ys)+',H'+xscale(e.end-e.start)+'V0')
.attr('stroke',lineColor)
.attr('fill','none');
g.classed('disulphide',true)
.attr('transform','translate(' + xscale(e.start) + ',0)');
var tt=makeBasicTooltip({title:'Annotation',Description:e.metadata.type,Span:e.metadata.start+' - '+e.metadata.end,Source:e.metadata.database});
break;
default:
var color=e.colour;
var lineColor=e.lineColour;
if(e.headStyle=='arrow'||e.headStyle=='pointer'||e.headStyle=='line') var strokeWidth=2;
else var strokeWidth=0;
g.append('path')
.attr('d','M'+0+','+0+',v'+(e.height*ys))
.attr('stroke',lineColor);
g.append('path')
.attr('d',PfamLollipopHead(0,ys*e.height,e.headStyle,lollipopHeadSize))
.attr('fill',color)
.attr('stroke',color)
.attr('strokeWidth',strokeWidth);
g.classed('lollipop',true)
.attr('transform','translate(' + xscale(e.start) + ',0)');
var tt=makeBasicTooltip({title:'Annotation',Description:e.metadata.description,Location:e.metadata.start,Source:e.metadata.database});
console.log(e.type);
break;
}
e.tooltip = tt;
g.classed('annotation scalable has-tooltip',true)
.on('mouseover',tooltip.show)
.on('mouseout',tooltip.hide);
return g.node();
}
function PfamRegion(r){
var x = xscale(Number(r.start));
var y = 0;
var w = xscale(r.end-r.start);
var h = opts.regionHeight;
var endLeft = r.endStyle;
var endRight = r.endStyle;
var s='M'+x+','+y;
var ry=h/2, rx=Math.min(h/2, w/2);
switch(endLeft){
case 'curved': s+='a'+rx+','+ry+',0,0,1,'+rx+','+(-ry);break;
case 'jagged': s+='l'+(rx/2)+','+(-ry/2)+','+(-rx/2)+','+(-ry/2);break;
case 'straight': s+='v'+(-ry); break;
case 'arrow': s+='l'+rx+','+(-ry); break;
}
switch(endRight){
case 'curved': s+='H'+(x+w-rx)+'a'+rx+','+ry+',0,0,1'+0+','+(2*ry);break;
case 'jagged': s+='H'+(x+w)+'l'+(-rx/2)+','+(ry/2)+','+(rx/2)+','+(ry/2)+','+(-rx/2)+','+(ry/2)+','+(rx/2)+','+(ry/2);break;
case 'straight': s+='H'+(x+w)+'v'+(2*ry); break;
case 'arrow': s+='l'+rx+','+ry+','+(-rx)+','+ry; break;
}
switch(endLeft){
case 'curved': s+='H'+(x+rx)+'a'+rx+','+ry+',0,0,1,'+(-rx)+','+(-ry);break;
case 'jagged': s+='H'+(x)+'l'+(rx/2)+','+(-ry/2)+','+(-rx/2)+','+(-ry/2);break;
case 'straight': s+='H'+(x)+'v'+(-ry); break;
case 'arrow': s+='l'+(-rx)+','+(-ry); break;
}
return s;
}
function PfamLollipopHead(cx,cy,type,diameter){
var r=diameter/2;
var s='M'+cx+','+cy;
switch(type){
case 'diamond': s+='m0,'+r+'l'+r+',-'+r+',-'+r+',-'+r+',-'+r+','+r+',z'; break;
case 'square': s+='m'+r+','+2+'v-'+diameter+',h-'+diameter+'v'+diameter+'z'; break;
case 'circle': s+='m0,-'+r+'a'+r+','+r+',0,1,1,0,'+diameter+'a'+r+','+r+',0,1,1,0,-'+diameter;break;
case 'arrow': s+='l'+r+','+r+',-'+r+',-'+r+',-'+r+','+r+','+r+',-'+r;break;
case 'pointer': s+='m0,'+(-1*cy)+'l'+r+',-'+r+',-'+r+','+r+',-'+r+',-'+r+','+r+','+r;break;
case 'line': s+='m0,'+diameter+'v-'+(3*diameter); break;
}
return s;
}
function setHeights(r,h,hs,s){
//set lollipop heights
var l=r.filter(function(a){return a.type!='disulphide';});
for(var i=0;i<l.length;++i){
l[i].height=h;
}
//set disulphide bridge heights
var d=r.filter(function(a){return a.type=='disulphide';});
d.sort(function(a,b){return a.start-b.start;});
var increment=opts.disulphideBridgeHeightIncrement;
for(var i=0;i<d.length;++i){
var prev=d.slice(0,i);
var ok=false;
var _this=d[i];
_this.height=h;
while(!ok && opts.disulphideBridgeHeightIncrement){
var collisions=prev.filter(function(e){
return _this.height==e.height && !( (e.start<_this.start&&e.end<_this.start) || (e.start>_this.end&&e.end>_this.end) );
});
collisions.length==0?ok=true:_this.height+=increment;
}
}
}
function toNumber(r){
var f=['regions','motifs','markups'];
var n=['start','end','aliStart','aliEnd'];
for(var i=0;i<f.length;++i)
for(var c=0;c<r[f[i]].length;++c)
for(var j=0;j<n.length;++j)
r[f[i]][c][n[j]]=Number(r[f[i]][c][n[j]]);
}
//Helpers - functions to perform useful tasks, exposed in the API
function pfamAjaxResults(callback){
function f(data,textStatus,jqXHR){
var response = data;
if(typeof(data)=="string") response=JSON.parse(response);
var r = response[0];
$.each(r.regions,function(i,e){
var tt=makeBasicTooltip({
title:'Region: '+e.metadata.identifier+' ('+e.metadata.accession+')',
Description:e.metadata.description,
Coordinates:e.metadata.start+' - '+e.metadata.end+' (alignment region '+e.metadata.aliStart+' - '+e.metadata.aliEnd+')',
Source:e.metadata.database
});
e.tooltip = tt;
});
callback(r);
}
return f;
};
function parseVariantString(geneName, variants){
m = variants.trim().split(/\s+/);
vArr = [];
for(ii=0;ii<m.length-2;ii+=3){
var gene=m[ii];
var cdna=m[ii+1];
var prot=m[ii+2];
if(!gene || !prot || !cdna) continue;
var codon = prot.match(/p.[a-zA-Z](\d+)/);
if(gene.toLowerCase() == geneName.toLowerCase() && codon){
vArr.push({
codon: codon[1],
pdot:prot,
cdna:cdna
});
}
}
return vArr;
}
function aggregate(variants, tooltipGenerator){
var m = d3.nest()
.key(function(d){return d.codon; })
.map(variants);
var nest = d3.nest()
.key(function(d){return d.codon; })
.key(function(d){return d.pdot; })
.entries(variants);
var arr=nest.map(function(e,i){
var parseAlteration=e.values[0].key.match(/(p\.\S\d+)/);
var wt=parseAlteration[0];
var wt_aa = wt.substr(2,1).toLowerCase();
var mut = {
codon:e.key,
count:m.get(e.key).filter(function(d){return d.pdot.slice(wt.length).toLowerCase() != wt_aa; }).length,
wildtype:wt
};
var alterations = e.values.map(function(e){
var m = e.key.match(/p\.\S\d+(.*)/);
var l = m[1];
if(l.length>=2 && l.substring(0,2)=="fs") l = 'fs';
else if(l.length>=2) l='in-frame';
return {
label:l,
count:e.values.length
};
}).filter(function(d){ return d.label.toLowerCase() != wt_aa; });
var nest=d3.nest()
.key(function(d){return d.label; })
.rollup(function(leaves){
return d3.sum(leaves,function(d){
return d.count;
})
})
.entries(alterations);
nest=nest.sort(function(a,b){
if(a.key=='other') {
return 1;
}
return b.value - a.value;
});
mut.nestedAlterations = nest;
if (tooltipGenerator) mut.tooltip = tooltipGenerator( mut);
return mut;
});
return arr;
}
//makeBasicTooltip expects an object with a "title" field. Other fields are added to a table, with fieldname as label and value as text
function makeBasicTooltip(obj){
var title=obj.title;
var d=obj;
delete d.title;
var el=$('<div>').css({border:'thin black solid',backgroundColor:'white',padding:'0.2em',display:'inline-block'});
var table=$('<table>').append($('<tr><th colspan=2 align="left">'+title+'</th></tr>')).appendTo(el);
$.each(d,function(name,value){table.append($('<tr><td>'+name+': </td><td>'+value+'</td></tr>'));});
return el;
}
//variantTable takes the results of a map operation on a nest
//expects codon number to be the key
function variantTable(mut){
var e = mut.nestedAlterations; //this is probably broken!
var ttinfo={
title:'Codon '+mut.wildtype,
'# of variants':mut.count,
'Distinct protein changes':e.length,
};
var v = e.sort(function(a,b){
return b.length - a.length; });