Commit 3b7a92a1 authored by Patrick Blumenkamp's avatar Patrick Blumenkamp
Browse files

integrate genome-viewer in genome-vuer

parent 86da9d7b
/*
* What follows is the result of much research on cross-browser styling.
* Credit left inline and big thanks to Nicolas Gallagher, Jonathan Neal,
* Kroc Camen, and the H5BP dev community and team.
*/
/* ==========================================================================
Base styles: opinionated defaults
========================================================================== */
html {
color: #222;
font-size: 1em;
line-height: 1.4;
}
/*
* Remove text-shadow in selection highlight:
* https://twitter.com/miketaylr/status/12228805301
*
* Vendor-prefixed and regular ::selection selectors cannot be combined:
* https://stackoverflow.com/a/16982510/7133471
*
* Customize the background color to match your design.
*/
::selection {
background: #b3d4fc;
text-shadow: none;
}
/*
* A better looking default horizontal rule
*/
hr {
display: block;
height: 1px;
border: 0;
border-top: 1px solid #ccc;
margin: 1em 0;
padding: 0;
}
/*
* Remove the gap between audio, canvas, iframes,
* images, videos and the bottom of their containers:
* https://github.com/h5bp/html5-boilerplate/issues/440
*/
audio,
canvas,
iframe,
img,
svg,
video {
vertical-align: middle;
}
/*
* Remove default fieldset styles.
*/
fieldset {
border: 0;
margin: 0;
padding: 0;
}
/*
* Allow only vertical resizing of textareas.
*/
textarea {
resize: vertical;
}
/* ==========================================================================
Browser Upgrade Prompt
========================================================================== */
.browserupgrade {
margin: 0.2em 0;
background: #ccc;
color: #000;
padding: 0.2em 0;
}
/* ==========================================================================
Author's custom styles
========================================================================== */
/* ==========================================================================
Helper classes
========================================================================== */
/*
* Hide visually and from screen readers
*/
.hidden {
display: none !important;
}
/*
* Hide only visually, but have it available for screen readers:
* https://snook.ca/archives/html_and_css/hiding-content-for-accessibility
*
* 1. For long content, line feeds are not interpreted as spaces and small width
* causes content to wrap 1 word per line:
* https://medium.com/@jessebeach/beware-smushed-off-screen-accessible-text-5952a4c2cbfe
*/
.visuallyhidden {
border: 0;
clip: rect(0 0 0 0);
height: 1px;
margin: -1px;
overflow: hidden;
padding: 0;
position: absolute;
width: 1px;
white-space: nowrap; /* 1 */
}
/*
* Extends the .visuallyhidden class to allow the element
* to be focusable when navigated to via the keyboard:
* https://www.drupal.org/node/897638
*/
.visuallyhidden.focusable:active,
.visuallyhidden.focusable:focus {
clip: auto;
height: auto;
margin: 0;
overflow: visible;
position: static;
width: auto;
white-space: inherit;
}
/*
* Hide visually and from screen readers, but maintain layout
*/
.invisible {
visibility: hidden;
}
/*
* Clearfix: contain floats
*
* For modern browsers
* 1. The space content is one way to avoid an Opera bug when the
* `contenteditable` attribute is included anywhere else in the document.
* Otherwise it causes space to appear at the top and bottom of elements
* that receive the `clearfix` class.
* 2. The use of `table` rather than `block` is only necessary if using
* `:before` to contain the top-margins of child elements.
*/
.clearfix:before,
.clearfix:after {
content: " "; /* 1 */
display: table; /* 2 */
}
.clearfix:after {
clear: both;
}
/* ==========================================================================
EXAMPLE Media Queries for Responsive Design.
These examples override the primary ('mobile first') styles.
Modify as content requires.
========================================================================== */
@media only screen and (min-width: 35em) {
/* Style adjustments for viewports that meet the condition */
}
@media print,
(min-resolution: 1.25dppx),
(min-resolution: 120dpi) {
/* Style adjustments for high resolution devices */
}
/* ==========================================================================
Print styles.
Inlined to avoid the additional HTTP request:
https://www.phpied.com/delay-loading-your-print-css/
========================================================================== */
@media print {
*,
*:before,
*:after {
background: transparent !important;
color: #000 !important; /* Black prints faster */
box-shadow: none !important;
text-shadow: none !important;
}
a,
a:visited {
text-decoration: underline;
}
a[href]:after {
content: " (" attr(href) ")";
}
abbr[title]:after {
content: " (" attr(title) ")";
}
/*
* Don't show links that are fragment identifiers,
* or use the `javascript:` pseudo protocol
*/
a[href^="#"]:after,
a[href^="javascript:"]:after {
content: "";
}
pre {
white-space: pre-wrap !important;
}
pre,
blockquote {
border: 1px solid #999;
page-break-inside: avoid;
}
/*
* Printing Tables:
* http://css-discuss.incutio.com/wiki/Printing_Tables
*/
thead {
display: table-header-group;
}
tr,
img {
page-break-inside: avoid;
}
p,
h2,
h3 {
orphans: 3;
widows: 3;
}
h2,
h3 {
page-break-after: avoid;
}
}
div.tooltip {
text-align: left;
font: 12px 'Roboto Mono', monospace;
background: black;
color: white;
border: 5px;
border-radius: 5px;
padding: 5px;
pointer-events: none;
position: fixed;
}
div.tooltip:after {
bottom: 100%;
left: 50%;
border: solid transparent;
content: " ";
color: black;
position: absolute;
pointer-events: none;
border-color: rgba(255, 255, 255, 0);
border-bottom-color: #000000;
border-width: 8px;
margin-left: -8px;
}
\ No newline at end of file
...@@ -7,13 +7,16 @@ ...@@ -7,13 +7,16 @@
<title></title> <title></title>
<meta name="description" content=""> <meta name="description" content="">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<script src="https://d3js.org/d3.v4.min.js"></script>
<script src="../lib/vue.js"></script> <script src="../lib/vue.js"></script>
<script src="./js/viz-linear-sequence.js" defer></script>
<link href="./css/viz-linear-sequence.css" rel="stylesheet">
</head> </head>
<body> <body>
<genome-viewer> <div id="app">
{{ message }} <genome-viewer/>
</genome-viewer> </div>
<script src="js/genome_viewer.js"></script> <script src="js/genome_viewer.js"></script>
</body> </body>
......
let genome_viewer = {
template: `
<div class="container-lin-dna">
<div id="linear-DNA-1" class="lin-dna" data-cluster-start=1706479 data-cluster-end=1718084 style="width: 100%; height: 50px;">
<div class="region-to-display" data-region-name="Gene 1" data-region-description="GMP synthase" data-region-start=1706479 data-region-end=1708024 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 2" data-region-description="glyoxalase" data-region-start=1708314 data-region-end=1708671 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 3" data-region-description="ABC transporter ATP-binding protein LlsG" data-region-start=1709429 data-region-end=1710317 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 4" data-region-description="ABC transporter permease protein LlsH" data-region-start=1710316 data-region-end=1711066 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 5" data-region-description="LlsX" data-region-start=1711106 data-region-end=1711424 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 6" data-region-description="SagB family dehydrogenase LlsB" data-region-start=1711420 data-region-end=1712296 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 7" data-region-description="LlsY" data-region-start=1712303 data-region-end=1713221 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 8" data-region-description="streptolysin-associated protein LlsD" data-region-start=1713213 data-region-end=1714527 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 9" data-region-description="hypothetical protein" data-region-start=1715351 data-region-end=1716125 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 10" data-region-description="glyoxalase family protein, N-terminal part" data-region-start=1716189 data-region-end=1716321 data-region-strand="+" data-region-type="gene">
</div>
<div class="region-to-display" data-region-name="Gene 11" data-region-description="hypothetical protein" data-region-start=1717235 data-region-end=1718084 data-region-strand="-" data-region-type="gene">
</div>
</div>
</div>`
}
var app = new Vue({ var app = new Vue({
el: '#app', el: '#app',
components: {
'genome-viewer': genome_viewer
},
data: { data: {
message: 'Hello Vue!' message: 'Hello Vue!'
} }
}) })
(function (d3) {
var div = d3.select( "body" )
.append( "div" )
.attr( "class", "tooltip" )
.style( "opacity", 0 );
Array.from( document.getElementsByClassName( "container-lin-dna" ) ).forEach( (e) => {
e.style.padding = '4rem 5rem';
} );
Array.from( document.getElementsByClassName( "lin-dna" ) ).forEach( (e) => {
const svgHeight = e.clientHeight;
const svgWidth = e.clientWidth;
const padding = 40;
//create axis
const xScale = d3.scaleLinear()
.domain( [ e.getAttribute( "data-cluster-start"), e.getAttribute( "data-cluster-end" ) ] )
.range( [ 0, svgWidth ] );
const xAxis = d3.axisBottom( xScale );
const svgContainer = d3.select(e).append( "svg" )
.attr( 'width', svgWidth + padding * 2 )
.attr( 'height', svgHeight + padding * 2 )
.append( "g" )
.attr( 'transform', 'translate(' + 0 + ',' + padding + ')' );
svgContainer.append( "g" )
.attr( 'transform', 'translate(' + 0 + ',' + 5 + ')' )
.call( xAxis );
//create visualization of DNA-Elements
const lineGenerator = d3.line();
svgContainer.selectAll('.arrow')
.data( collectDNARegionData( e ) )
.enter()
.append( 'path' )
.attr( 'class', 'arrow' )
.attr( 'data-toggle', 'tooltip' )
.attr( 'data-placement', 'bottom' )
.attr('d', d => { return lineGenerator( returnRegionAreaPoints( d, xScale ) ) } )
.style( 'fill', d => { return returnSectionColor( d.type ) } )
.style( 'opacity', 0.6 )
.on( "mouseover", function(d) {
this.style.opacity = 1;
div.style( "opacity", .9 )
.style( "width", "220px")
.style( "left", ( this.getBoundingClientRect().x + ( this.getBoundingClientRect().width / 2 ) - 110 ) + "px" )
.style( "top", ( this.getBoundingClientRect().bottom + 10 ) + "px" );
div.html( d => returnStringForPopup( this.__data__ ) )
})
.on( "mouseout", function(d) {
this.style.opacity = 0.6;
div.style( "opacity", 0 );
});
} );
} )(d3);
function returnStringForPopup( regionElement ){
var text = "";
//build table
text = text.concat( "<table><tbody><tr><td style=\"vertical-align:top\"><b>Name</b>:</td><td>" + regionElement.name + "</td></tr>" )
text = text.concat( "<tr><td style=\"vertical-align:top\"><b>Desc</b>:</td><td>" + regionElement.desc + "</td></tr>" )
text = text.concat( "<tr><td style=\"vertical-align:top\"><b>Start</b>:</td><td>" + regionElement.start + "</td></tr>" )
text = text.concat( "<tr><td style=\"vertical-align:top\"><b>End</b>:</td><td>" + regionElement.end + "</td></tr>" )
text = text.concat( "<tr><td style=\"vertical-align:top\"><b>Type</b>:</td><td>" + regionElement.type + "</td></tr>" )
Array.from( Object.keys( regionElement ) ).forEach( key => {
if( key.match( "data-optional-" ) ){
text = text.concat( "<tr><td style=\"vertical-align:top\"><b>" + key.replace( "data-optional-", "" ) + "</b>:</td><td> " + regionElement[ key ] + "</td></tr>" )
}
} )
text = text.concat( "</tbody></table>" )
return text;
}
function returnSectionColor( type ) {
switch ( type ) {
case 'region': return '#bdbdbd' // greyLighten
case 'gene': return '#757575' // greyDarken
case 'cds': return '#000000' // black
case 'rRNA': return '#795548' // brown
case 'tRNA': return '#4caf50' // green
case 'ncRNA': return '#ff9800' // orange
default: return -1
}
}
function collectDNARegionData( clusterElement ) {
var data = [];
Array.from( clusterElement.getElementsByClassName( "region-to-display" ) ).forEach( (e) => {
var regionData = {
"name": e.getAttribute( "data-region-name" ),
"desc": e.getAttribute( "data-region-description" ),
"start": e.getAttribute( "data-region-start" ),
"end": e.getAttribute( "data-region-end" ),
"strand": e.getAttribute( "data-region-strand" ),
"type": e.getAttribute( "data-region-type" )
};
Array.from( e.attributes ).forEach( (attr) => {
if( attr.name.match( "data-optional-" ) ){
regionData[ attr.name ] = attr.value
console.log( regionData[ attr.name ] )
}
} );
data.push( regionData );
} );
return data;
}
function returnRegionAreaPoints( data, xScale ) {
const peakWidth = 10;
const height = -40;
const mid = height / 2;
let points = [];
//check for correct data type and strand
if( returnSectionColor( data.type ) !== -1 && ( data.strand === "+" || data.strand === "-" ) ){
//return drawing points
if( data.type === 'region' ) {
points = [
[ xScale( data.start ), 0 ],
[ xScale( data.end ), 0 ],
[ xScale( data.end ), height ],
[ xScale( data.start ), height ]
];
} else if ( xScale( data.end ) - xScale( data.start ) <= peakWidth ) {
//draw short arrows (without shaft)
if ( data.strand === "+" ) {
points = [
[ xScale( data.start ), 0 ],
[ xScale( data.end ), mid ],
[ xScale( data.start ), height ]
]
} else if ( data.strand === "-" ) {
points = [
[ xScale( data.end ), 0 ],
[ xScale( data.start ), mid ],
[ xScale( data.end ), height ]
]
}
} else {
//draw longer arrows (with shaft)
if ( data.strand === "+" ) {
points = [
[ xScale( data.start ), 0 ],
[ xScale( data.end ) - peakWidth, 0 ],
[ xScale( data.end ), mid ],
[ xScale( data.end ) - peakWidth, height ],
[ xScale( data.start ), height ]
]
} else if ( data.strand === "-" ) {
points = [
[ xScale( data.start ), mid],
[ xScale( data.start ) + peakWidth, 0 ],
[ xScale( data.end ), 0 ],
[ xScale( data.end ), height ],
[ xScale( data.start ) + peakWidth, height ]
]
}
}
} else {
console.log( `Unknown type: "` + data.type + `" or unknown strand: "` + data.strand + `"` );
}
return points;
}
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