Edit in JSFiddle

$(function(){
  
  var $container = $('#container'),
      $checkboxes = $('#filters input');
  
  $container.isotope({
    itemSelector: '.item',
    // filter red items first
    filter: '.red'
  });
  
  $checkboxes.change(function(){
    var filters = [];
    // get checked checkboxes values
    $checkboxes.filter(':checked').each(function(){
      filters.push( this.value );
    });
    // ['.red', '.blue'] -> '.red, .blue'
    filters = filters.join(', ');
    $container.isotope({ filter: filters });
  });
    
  $('#shuffle').click(function(){
    $container.isotope('shuffle');
  });
    
});

<div id="filters">
  <input type="checkbox" name="red" value=".red" id="red" checked><label for="red">red</label>
  <input type="checkbox" name="blue" value=".blue" id="blue"><label for="blue">blue</label>
  <input type="checkbox" name="green" value=".green" id="green"><label for="green">green</label>
  <input type="checkbox" name="yellow" value=".yellow" id="yellow"><label for="yellow">yellow</label>
</div>

<p><button id="shuffle">Shuffle</button></p>

<div id="container">
  <div class="item red"></div>
  <div class="item blue"></div>
  <div class="item green"></div>
  <div class="item yellow"></div>
  <div class="item red"></div>
  <div class="item blue"></div>
  <div class="item green"></div>
  <div class="item yellow"></div>
  <div class="item red"></div>
  <div class="item blue"></div>
  <div class="item green"></div>
  <div class="item yellow"></div>
  <div class="item red"></div>
  <div class="item blue"></div>
  <div class="item green"></div>
  <div class="item yellow"></div>
  <div class="item red"></div>
  <div class="item blue"></div>
  <div class="item green"></div>
  <div class="item yellow"></div>
</div>

body {
  font-family: 'Helvetica Neue', Arial, sans-serif;
}

#container {
  border: 1px solid;
  padding: 3px;
}

.item {
  width: 70px;
  height: 70px;
  margin: 3px;
  float: left;
}

.item.next {
  width: 60px;
  height: 60px;
  border: 5px solid black;
  border-radius: 35px;
}

.red { background: red; }
.blue { background: blue; }
.green { background: green; }
.yellow { background: yellow; }

/* Start: Recommended Isotope styles */

/**** Isotope Filtering ****/

.isotope-item {
  z-index: 2;
}

.isotope-hidden.isotope-item {
  pointer-events: none;
  z-index: 1;
}

/**** Isotope CSS3 transitions ****/

.isotope,
.isotope .isotope-item {
  -webkit-transition-duration: 0.8s;
     -moz-transition-duration: 0.8s;
          transition-duration: 0.8s;
}

.isotope {
  -webkit-transition-property: height, width;
     -moz-transition-property: height, width;
          transition-property: height, width;
}

.isotope .isotope-item {
  -webkit-transition-property: -webkit-transform, opacity;
     -moz-transition-property:    -moz-transform, opacity;
          transition-property:         transform, opacity;
}

/**** disabling Isotope CSS3 transitions ****/

.isotope.no-transition,
.isotope.no-transition .isotope-item,
.isotope .isotope-item.no-transition {
  -webkit-transition-duration: 0s;
     -moz-transition-duration: 0s;
          transition-duration: 0s;
}

/* End: Recommended Isotope styles */