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export_html_result.html
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<!DOCTYPE html>
<meta charset="utf-8">
<html>
<head>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js"></script>
<script src="https://d3js.org/d3.v4.min.js"></script>
<style>
.axis path {
display: none;
}
.pixel {
/* image-rendering: pixelated; */
padding: 0px;
margin: 0px;
border: 0px;
image-rendering: optimizeSpeed; /* STOP SMOOTHING, GIVE ME SPEED */
image-rendering: -moz-crisp-edges; /* Firefox */
image-rendering: -o-crisp-edges; /* Opera */
image-rendering: -webkit-optimize-contrast; /* Chrome (and eventually Safari) */
image-rendering: pixelated; /* Chrome */
image-rendering: optimize-contrast; /* CSS3 Proposed */
-ms-interpolation-mode: nearest-neighbor; /* IE8+ */
}
.axis line {
stroke-opacity: 0.3;
shape-rendering: crispEdges;
}
.line {
fill: none;
stroke: steelblue;
stroke-width: 2px;
}
</style>
<script>
$(document).ready(function() {
var yticklabels = ['NA'];
var ids = ['NA'];
var samples = ['NA'];
var vlines = [];
var xtick_pos = [];
var xtick_labels = [];
var field_name = '';
var title_text = 'Experiment';
//**********************************************************
// following variables are set by the external python program
// DO NOT DELETE/CHANGE
var yticklabels = ["k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__","k__Bacteria; p__Tenericutes; c__Mollicutes; o__Mycoplasmatales; f__Mycoplasmataceae; g__Mycoplasma; s__","k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Oxalobacteraceae; g__Janthinobacterium; s__lividum","k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Variovorax; s__paradoxus","k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__Veillonella; s__","k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__Flavobacteriaceae; g__Capnocytophaga; s__","k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Actinomycetaceae; g__Actinomyces; s__","k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__; s__","k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Bulleidia; s__moorei","k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales","Unknown","bad_bacteria"];
var ids = ["AA","AT","AG","AC","TA","TT","TG","TC","GA","GT","GG","badfeature"];
var samples = ["S1","S2","S3","S4","S5","S6","S7","S8","S9","S10","S11","S12","S13","S14","S15","S16","S17","S18","S19","S20","badsample"];
var vlines = ["11.0","20.0"];
var xtick_pos = ["5.5","15.5","20.5"];
var xtick_labels = ["1","2","nan"];
var field_name = "group";
var title_text = "the heatmap";
//***********************************************************
var yaxiswidth = 100;
var xaxisheight = 20;
// set the title
$('#field_name').html(field_name);
$('#title_text').html(title_text);
var svg = d3.select('svg');
var width = $('#div-heatmap').width();
var height = $('#div-heatmap').height();
// available display for the heatmap (without axes)
var hwidth = width - yaxiswidth;
var hheight = height - xaxisheight;
svg.attr('width', width)
.attr('height', height);
svg.on('click', onclick);
var xScale = d3.scaleLinear()
.domain([0, width])
.range([0, width]);
var yScale = d3.scaleLinear()
.domain([0, ids.length])
.range([0.5, hheight + 0.5]);
var heatmapregion = svg
.append('svg')
.attr('width', width - yaxiswidth + 'px')
.attr('height', height - xaxisheight + 'px')
.attr('x', yaxiswidth)
.attr('y', 0);
var heatmap = heatmapregion.append('g')
.append('image')
.attr('class', 'pixel')
.attr('width', samples.length)
.attr('height', ids.length)
.attr('xlink:xlink:href', 'data:image/png;base64, iVBORw0KGgoAAAANSUhEUgAAABUAAAAMCAYAAACNzvbFAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAuIwAALiMBeKU/dgAAADl0RVh0U29mdHdhcmUAbWF0cGxvdGxpYiB2ZXJzaW9uIDIuMS4yLCBodHRwOi8vbWF0cGxvdGxpYi5vcmcvNQv5yAAAAVJJREFUKJG1kb9KA0EQxn%2BzexvOhBCVXBQRFQQrsbJQ6zyCtT6FL2CtYGFjJQiCNhaWPkASQRRBSzGkECsV/5x6ub21uAgmBDWgH3wMM3w7882szC6vO3pA/071R40XDkkvPWFp/keJlGXReRNj2IE8NmewWQ%2BbUSQZwRoh8cBpIdHpA6dbVGndKdqIgAcQ1xtQB0VK842Lhzan3S/n3awsgANJOmhdK6ZUtrWadagYdNOhIoeOEnQYo1%2Ba6Psn4noDFZxHjKxVKF5EDG9UCE5DSpsVSrVHiltV%2Bu4SBrer6RDrKOzWeO8XsgfHhIHGHJ1wO5fFnV3yOlVKB0/ur/b0%2B7%2BBHF5NO43DInyNn%2BjMu6FTI2VZ/HOn6q8bAnjXezOMB/eM5h4oZp4pmmcKOiSv38irV3LqHV%2Ba%2BBID4IvFF4sR8EUwCEYURjQeGi3qf9b/AD5ffIoFOyZjAAAAAElFTkSuQmCC')
var xyratio = get_xyratio();
var scalex = 1;
var scaley = 1;
var xAxis = d3.axisBottom(xScale)
.tickValues(xtick_pos)
.tickFormat(function(d, i) {return xtick_labels[i];});
function customTickFunction(d) {
var dom = yAxis.scale().domain();
if ((dom[1] - dom[0]) < 50) {
return Math.round(dom[1] - dom[0]);
}
return 50;
}
var yAxis = d3.axisLeft(yScale)
.ticks(50)
.tickFormat(function(d) {
try {
var taxa = yticklabels[Math.round(d)].replace(/;+$/, '').split(';');
var label = taxa.pop();
while (label.length == 3 && label.substring(1,3) == '__') {
label = taxa.pop()
}
if (taxa.length > 0) {
label = taxa.pop() + ' ' + label;
}
}
catch(err) {
label=''
}
return label;
});
yAxis.ticks(customTickFunction());
var gY = svg.append('g')
.attr('class', 'axis axis--y')
.attr('transform', 'translate(' + yaxiswidth + ',0)')
.call(yAxis);
var gX = svg.append('g')
.attr('class', 'axis axis--x')
.attr('transform', 'translate(' + yaxiswidth + ',' + (hheight) + ')')
.call(xAxis);
// The per sample-type vlines
var vline_lines = heatmapregion.append('g');
for (idx=0;idx<vlines.length; idx++) {
vline_lines.append('line')
.attr('id', 'vline')
.attr('class', 'vLine')
.style('stroke', 'white')
// .style('stroke-dasharray', '1,1')
.style('stroke-opacity', 1)
.style('stroke-width', 6 * xyratio)
.attr('x1', vlines[idx]).attr('y1', 0)
.attr('x2', vlines[idx]).attr('y2', ids.length);
}
// The cursor crosshair
var focus = heatmapregion.append('g');
var xline = focus.append('line')
.attr('id', 'focusLineX')
.attr('class', 'focusLine')
.style('stroke', 'white')
// .style('stroke-dasharray', '1,1')
.style('stroke-opacity', 0.5)
.style('stroke-width', 1);
focus.append('line')
.attr('id', 'focusLineY')
.attr('class', 'focusLine')
.style('stroke', 'white')
.style("stroke-opacity", 0.5)
// .style('stroke-dasharray', '1,1')
.style('stroke-width', 1 * xyratio);
d3.select('#reset')
.on('click', resetted);
d3.select('#zoomsplus')
.on('click', zoomX);
d3.select('#zoomsminus')
.on('click', unzoomX);
d3.select('#zoomfplus')
.on('click', zoomY);
d3.select('#zoomfminus')
.on('click', unzoomY);
d3.select('#movedown')
.on('click', moveDown);
d3.select('#moveup')
.on('click', moveUp);
d3.select('#moveright')
.on('click', moveRight);
d3.select('#moveleft')
.on('click', moveLeft);
var initial_scale_factor = hwidth / samples.length;
var shiftdown = 0;
var current_tx, current_scale_x, current_scale_y, current_ty;
d3.select('body').on('keydown', onkeydown);
d3.select('body').on('keyup', onkey);
var zoom = d3.zoom()
.scaleExtent([initial_scale_factor, 10000])
.translateExtent([[0, 0], [width / initial_scale_factor, 100000000]])
.on('zoom', zoomed);
heatmapregion.call(zoom);
// and initial zoom to have full screen
resetted();
function onkeydown() {
if (d3.event.key == '-') {
unzoomY();
return;
};
if (d3.event.key == '=') {
zoomY();
return;
};
if (d3.event.key == '+') {
zoomX();
return;
};
if (d3.event.key == '_') {
unzoomX();
return;
};
if (d3.event.key == 'ArrowDown') {
moveDown();
return;
};
if (d3.event.key == 'ArrowUp') {
moveUp();
return;
};
if (d3.event.key == 'ArrowLeft') {
moveLeft();
return;
};
if (d3.event.key == 'ArrowRight') {
moveRight();
return;
};
// and now process the shift
onkey();
}
function onkey() {
shiftdown = d3.event.shiftKey;
if (shiftdown) {
xyratio = xyratio * current_scale_y / current_scale_x;
current_scale_y = current_scale_x;
current_tx = current_tx / (current_scale_x);
} else {
xyratio = xyratio * current_scale_y / current_scale_x;
current_ty = current_ty / current_scale_x;
}
}
function zoomed() {
tt = d3.event.transform
// if shift pressed we're in x-axis zoom/move mode
if (shiftdown != 0) {
current_tx = tt.x;
current_scale_x = tt.k;
gX.call(xAxis.scale(d3.event.transform.rescaleX(xScale)));
vline_lines.selectAll('#vline').style('stroke-width', 3 / tt.k);
focus.selectAll('#focusLineY').style('stroke-width', 2 / tt.k);
};
// if no shift pressed - we're in y-axis move/zoom mode
if (shiftdown != 1) {
current_ty = tt.y;
current_scale_y = tt.k;
ytransform = d3.zoomIdentity.translate(tt.x, tt.y).scale(tt.k * xyratio);
// for the y-axis we need to update the scale since it's already scaled by ids/hheight
ytransform2 = d3.zoomIdentity.translate(tt.x, tt.y).scale(tt.k * xyratio * ids.length / hheight);
gY.call(yAxis.scale(ytransform2.rescaleY(yScale)).ticks(customTickFunction()));
focus.selectAll('#focusLineX').style('stroke-width', 2 / (xyratio * tt.k));
};
newt = 'translate(' + current_tx + ',' + current_ty + ') scale(' + current_scale_x + ',' + current_scale_y * xyratio + ')';
heatmap.attr('transform', newt);
vline_lines.attr('transform', newt);
focus.attr('transform', newt);
}
function reset_coords() {
xyratio = get_xyratio();
current_tx = 0;
current_scale_x = initial_scale_factor;
current_ty = 0;
current_scale_y = initial_scale_factor;
}
function resetted() {
console.log('reset coordinates');
reset_coords();
old_shiftdown = shiftdown;
shiftdown = 2;
heatmapregion.call(zoom.transform, d3.zoomIdentity.scale(initial_scale_factor));
shiftdown = old_shiftdown;
// The nice transition didn't work with the shift up/down
// heatmapregion.transition()
// .duration(750)
// .call(zoom.transform, d3.zoomIdentity.scale(initial_scale_factor));
}
function zoomX() {
old_shiftdown = shiftdown;
shiftdown = 1;
ctrans = d3.zoomTransform(heatmapregion.node());
ctrans.x = 0;
ctrans.k = ctrans.k * 2;
// the leftmost feature showing in the screen
screen_start = xAxis.scale().invert(0);
// move so 0th sample is left column displaying
heatmapregion.call(zoom.transform, ctrans);
zoom.translateBy(heatmapregion, 0, 0);
zoom.scaleBy(heatmapregion,1);
newpos = xAxis.scale()(screen_start);
newpos = -newpos;
ctrans.x = newpos;
heatmapregion.call(zoom.transform, ctrans);
shiftdown = old_shiftdown;
}
function unzoomX() {
old_shiftdown = shiftdown;
shiftdown = 1;
ctrans = d3.zoomTransform(heatmapregion.node());
ctrans.x = 0;
ctrans.k = ctrans.k / 2
// the topmost feature showing in the screen
screen_start = xAxis.scale().invert(0);
// move so 0th feature is top row displaying
// zoom.translateBy(heatmapregion, 0, -tozero/xyratio)
heatmapregion.call(zoom.transform, ctrans);
zoom.translateBy(heatmapregion, 0, 0);
zoom.scaleBy(heatmapregion,1);
newpos = xAxis.scale()(screen_start);
newpos = -newpos;
ctrans.x = newpos;
heatmapregion.call(zoom.transform, ctrans);
shiftdown = old_shiftdown;
}
function zoomY() {
ctrans = d3.zoomTransform(heatmapregion.node());
ctrans.y = 0;
// the topmost feature showing in the screen
screen_start = yAxis.scale().invert(0);
// move so 0th feature is top row displaying
// zoom.translateBy(heatmapregion, 0, -tozero/xyratio)
heatmapregion.call(zoom.transform, ctrans);
xyratio = xyratio * 2;
zoom.translateBy(heatmapregion, 0, 0);
newpos = yAxis.scale()(screen_start);
newpos = -newpos;
ctrans.y = newpos;
heatmapregion.call(zoom.transform, ctrans);
}
function unzoomY() {
ctrans = d3.zoomTransform(heatmapregion.node());
ctrans.y = 0;
// the topmost feature showing in the screen
screen_start = yAxis.scale().invert(0);
// move so 0th feature is top row displaying
// zoom.translateBy(heatmapregion, 0, -tozero/xyratio)
heatmapregion.call(zoom.transform, ctrans);
xyratio = xyratio / 2;
zoom.translateBy(heatmapregion, 0, 0);
newpos = yAxis.scale()(screen_start);
newpos = -newpos;
ctrans.y = newpos;
heatmapregion.call(zoom.transform, ctrans);
}
function moveDown() {
screen_start = yAxis.scale().invert(0);
screen_end = yAxis.scale().invert(height - xaxisheight);
old_shiftdown = shiftdown
shiftdown = 0;
zoom.translateBy(heatmapregion, 0, (screen_start - screen_end) * xyratio);
shiftdown = old_shiftdown;
}
function moveUp() {
screen_start = yAxis.scale().invert(0);
screen_end = yAxis.scale().invert(height - xaxisheight);
old_shiftdown = shiftdown
shiftdown = 0;
zoom.translateBy(heatmapregion, 0, (screen_end - screen_start) * xyratio);
shiftdown = old_shiftdown;
}
function moveLeft() {
screen_start = xAxis.scale().invert(0);
screen_end = xAxis.scale().invert(width - xaxisheight);
old_shiftdown = shiftdown
shiftdown = 1;
zoom.translateBy(heatmapregion, (screen_end - screen_start), 0);
shiftdown = old_shiftdown;
}
function moveRight() {
screen_start = xAxis.scale().invert(0);
screen_end = xAxis.scale().invert(width - xaxisheight);
old_shiftdown = shiftdown
shiftdown = 1;
zoom.translateBy(heatmapregion, (screen_start - screen_end), 0);
shiftdown = old_shiftdown;
}
function onclick() {
var pos = d3.mouse(heatmap.node());
// var cx = Math.round(xScale.invert(pos[0])), cy = Math.round(yScale.invert(pos[1]));
var cx = Math.round(pos[0]-0.5), cy = Math.round(pos[1]-0.5);
// var posx = xScale.invert(pos[0]), posy = yScale.invert(pos[1]);
var posx = pos[0], posy = pos[1];
focus.select('#focusLineY')
.attr('x1', Math.round(posx + 0.5) - 0.5).attr('y1', 0)
.attr('x2', Math.round(posx + 0.5) - 0.5).attr('y2', ids.length);
focus.select('#focusLineX')
.attr('x1', 0).attr('y1', Math.round(posy-0.5) + 0.5)
.attr('x2', samples.length).attr('y2', Math.round(posy-0.5) + 0.5);
var cid = ids[cy];
var csamp = samples[cx];
try {
var ctax = yticklabels[cy].split(';').map(function(e) {
try {
e = e.split('_').pop()
} catch(err) {
console.log('failed to split taxonomy on "_":');
console.log(e)
console.log(err)
}
return '<a href="https://en.wikipedia.org/wiki/' + e + '" target="_blank">' + e + '</a>'
}).join('; ');
} catch (err) {
console.log('error when parsing taxonomy:');
console.log(err);
ctax = "No taxonomy in biom table";
}
$('#taxonomy').html(ctax);
$('#sampleid').html(csamp);
$('#sequence').html(cid);
// Get dbBact annotations for selection
$.ajax({
url: 'http://api.dbbact.org/sequences/get_string_annotations',
type: 'POST',
data: JSON.stringify({'sequence': cid}),
dataType: 'json',
contentType: 'application/json; charset=utf-8',
success: function(data) {
if (data.annotations.length == 0) {
atext = 'No annotations found for sequence'
}
else {
var atext = '';
var clink = 'http://dbbact.org/sequence_annotations/' + cid;
var ctext = '<p><a href="' + clink + '" target="_blank">dbBact Summary</a></p>';
atext += ctext;
for (i = 0; i < data.annotations.length; i++) {
clink = 'http://dbbact.org/annotation_info/' + data.annotations[i].annotationid.toString();
ctext = '<a href="' + clink + '" target="_blank">' + data.annotations[i].annotation_string + '</a><br>';
atext += ctext;
}
}
$('#p-annotation').html(atext);
}
});
}
function get_xyratio() {
return (hheight / ids.length) * (samples.length / hwidth);
}
$(window).on('resize', function(){
$('body').height('calc(100vh - 50px)');
});
});
</script>
</head>
<body style="height: calc(100vh - 50px); min-height: 600px; min-width: 1080px;">
<div> </div>
<div id="div-annotation" class="panel panel-default" style="float: right; margin: 10px; width: 360px; height: auto; white-space: nowrap;">
<!--Here goes the annotations!-->
<div class="panel-heading">
<b>dbBact annotations</b>
</div>
<div class="panel-body" style="overflow: auto;">
<p id="p-annotation">Click on heatmap to see annotations</p>
</div>
<div class="panel-footer">
For more analysis options, download <a href='https://github.com/amnona/calour' target='_blank'>Calour</a>.
</div>
</div>
<div class="panel panel-default" style="margin: 10px; width: auto; height: 100%; overflow: hidden;">
<div id="div-title" class="panel-heading">
<b><span id="title_text">Experiment</span></b>
(sorted by field: <b><span id='field_name'> NA </span></b>)
<span style="float: right;">
<button id="reset" class="btn btn-default btn-xs">Reset</button>
<button id="zoomfplus" class="btn btn-default btn-xs">F+</button>
<button id="zoomfminus" class="btn btn-default btn-xs">F-</button>
<button id="zoomsplus" class="btn btn-default btn-xs">S+</button>
<button id="zoomsminus" class="btn btn-default btn-xs">S-</button>
<button id="moveup" class="btn btn-default btn-xs">↑</button>
<button id="movedown" class="btn btn-default btn-xs">↓</button>
<button id="moveleft" class="btn btn-default btn-xs">←</button>
<button id="moveright" class="btn btn-default btn-xs">→</button>
<button id="btn-help" class="btn btn-default btn-xs" onclick="$('#div-help').toggle();">Help</button>
</span>
</div>
<div id="div-heatmap" class="panel-body" style="height: calc(100% - 100px);">
<svg id="heatmap" style="width: 100%; height: 100%;)"></svg>
</div>
<div id="div-selection" class="panel-footer">
<!--Here goes the selection!-->
<span style="display: inline-block; float: left; overflow: hidden;"><b>Sample: </b></span>
<span id="sampleid" style="display: inline-block; float: left; width: 120px; overflow: auto; white-space: nowrap;">NA</span>
<span style="display: inline-block; float: left; overflow: hidden;"> <b>Taxonomy: </b></span>
<span id="taxonomy" style="display: block; overflow: auto; white-space: nowrap;">NA</span>
<span style="display: inline-block; float: left; overflow: hidden;"><b>Sequence: </b></span>
<span id="sequence" style="display: block; overflow: auto; white-space: nowrap;">NA</span>
</div>
</div>
<div id="div-help" class="panel panel-info" style="display: none; position: fixed; left: 50%; width: 400px; margin-left: -200px; top: 200px; box-shadow: 10px 10px 5px rgba(0,0,0,0.5);">
<div class="panel-heading">
Help
<span style="float: right;"><button class="btn btn-default btn-xs" onclick="$('#div-help').hide();">×</button></span>
</div>
<div class="panel-body">
<p>Use mouse or -/= for zooming bacteria, shift+mouse or _/+ for zooming samples, arrow keys to move in heatmap.</p>
</div>
</div>
</body>
</html>