Log In Sign Up
Models:
Alyssa Salazar
AlyssaS/
VoltRon
0
Downloads: 1
Diff of /docs/ondisk.html [000000] .. [413088]

Switch to unified view

a b/docs/ondisk.html 

  1
  
<!DOCTYPE html>





  
  

  2
  





  
  

  3
  
<html>





  
  

  4
  





  
  

  5
  
<head>





  
  

  6
  





  
  

  7
  
<meta charset="utf-8" />





  
  

  8
  
<meta name="generator" content="pandoc" />





  
  

  9
  
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />





  
  

  10
  





  
  

  11
  





  
  

  12
  





  
  

  13
  





  
  

  14
  
<title>ondisk</title>





  
  

  15
  





  
  

  16
  
<script src="site_libs/header-attrs-2.29/header-attrs.js"></script>





  
  

  17
  
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>





  
  

  18
  
<meta name="viewport" content="width=device-width, initial-scale=1" />





  
  

  19
  
<link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />





  
  

  20
  
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>





  
  

  21
  
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>





  
  

  22
  
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>





  
  

  23
  
<style>h1 {font-size: 34px;}





  
  

  24
  
       h1.title {font-size: 38px;}





  
  

  25
  
       h2 {font-size: 30px;}





  
  

  26
  
       h3 {font-size: 24px;}





  
  

  27
  
       h4 {font-size: 18px;}





  
  

  28
  
       h5 {font-size: 16px;}





  
  

  29
  
       h6 {font-size: 12px;}





  
  

  30
  
       code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}





  
  

  31
  
       pre:not([class]) { background-color: white }</style>





  
  

  32
  
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>





  
  

  33
  
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />





  
  

  34
  
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>





  
  

  35
  
<script src="site_libs/navigation-1.1/tabsets.js"></script>





  
  

  36
  
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />





  
  

  37
  
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>





  
  

  38
  
<link href="site_libs/font-awesome-6.5.2/css/all.min.css" rel="stylesheet" />





  
  

  39
  
<link href="site_libs/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet" />





  
  

  40
  





  
  

  41
  
<style type="text/css">





  
  

  42
  
  code{white-space: pre-wrap;}





  
  

  43
  
  span.smallcaps{font-variant: small-caps;}





  
  

  44
  
  span.underline{text-decoration: underline;}





  
  

  45
  
  div.column{display: inline-block; vertical-align: top; width: 50%;}





  
  

  46
  
  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}





  
  

  47
  
  ul.task-list{list-style: none;}





  
  

  48
  
    </style>





  
  

  49
  





  
  

  50
  
<style type="text/css">code{white-space: pre;}</style>





  
  

  51
  
<script type="text/javascript">





  
  

  52
  
if (window.hljs) {





  
  

  53
  
  hljs.configure({languages: []});





  
  

  54
  
  hljs.initHighlightingOnLoad();





  
  

  55
  
  if (document.readyState && document.readyState === "complete") {





  
  

  56
  
    window.setTimeout(function() { hljs.initHighlighting(); }, 0);





  
  

  57
  
  }





  
  

  58
  
}





  
  

  59
  
</script>





  
  

  60
  





  
  

  61
  





  
  

  62
  





  
  

  63
  





  
  

  64
  





  
  

  65
  





  
  

  66
  





  
  

  67
  





  
  

  68
  





  
  

  69
  
<style type = "text/css">





  
  

  70
  
.main-container {





  
  

  71
  
  max-width: 940px;





  
  

  72
  
  margin-left: auto;





  
  

  73
  
  margin-right: auto;





  
  

  74
  
}





  
  

  75
  
img {





  
  

  76
  
  max-width:100%;





  
  

  77
  
}





  
  

  78
  
.tabbed-pane {





  
  

  79
  
  padding-top: 12px;





  
  

  80
  
}





  
  

  81
  
.html-widget {





  
  

  82
  
  margin-bottom: 20px;





  
  

  83
  
}





  
  

  84
  
button.code-folding-btn:focus {





  
  

  85
  
  outline: none;





  
  

  86
  
}





  
  

  87
  
summary {





  
  

  88
  
  display: list-item;





  
  

  89
  
}





  
  

  90
  
details > summary > p:only-child {





  
  

  91
  
  display: inline;





  
  

  92
  
}





  
  

  93
  
pre code {





  
  

  94
  
  padding: 0;





  
  

  95
  
}





  
  

  96
  
</style>





  
  

  97
  





  
  

  98
  





  
  

  99
  
<style type="text/css">





  
  

  100
  
.dropdown-submenu {





  
  

  101
  
  position: relative;





  
  

  102
  
}





  
  

  103
  
.dropdown-submenu>.dropdown-menu {





  
  

  104
  
  top: 0;





  
  

  105
  
  left: 100%;





  
  

  106
  
  margin-top: -6px;





  
  

  107
  
  margin-left: -1px;





  
  

  108
  
  border-radius: 0 6px 6px 6px;





  
  

  109
  
}





  
  

  110
  
.dropdown-submenu:hover>.dropdown-menu {





  
  

  111
  
  display: block;





  
  

  112
  
}





  
  

  113
  
.dropdown-submenu>a:after {





  
  

  114
  
  display: block;





  
  

  115
  
  content: " ";





  
  

  116
  
  float: right;





  
  

  117
  
  width: 0;





  
  

  118
  
  height: 0;





  
  

  119
  
  border-color: transparent;





  
  

  120
  
  border-style: solid;





  
  

  121
  
  border-width: 5px 0 5px 5px;





  
  

  122
  
  border-left-color: #cccccc;





  
  

  123
  
  margin-top: 5px;





  
  

  124
  
  margin-right: -10px;





  
  

  125
  
}





  
  

  126
  
.dropdown-submenu:hover>a:after {





  
  

  127
  
  border-left-color: #adb5bd;





  
  

  128
  
}





  
  

  129
  
.dropdown-submenu.pull-left {





  
  

  130
  
  float: none;





  
  

  131
  
}





  
  

  132
  
.dropdown-submenu.pull-left>.dropdown-menu {





  
  

  133
  
  left: -100%;





  
  

  134
  
  margin-left: 10px;





  
  

  135
  
  border-radius: 6px 0 6px 6px;





  
  

  136
  
}





  
  

  137
  
</style>





  
  

  138
  





  
  

  139
  
<script type="text/javascript">





  
  

  140
  
// manage active state of menu based on current page





  
  

  141
  
$(document).ready(function () {





  
  

  142
  
  // active menu anchor





  
  

  143
  
  href = window.location.pathname





  
  

  144
  
  href = href.substr(href.lastIndexOf('/') + 1)





  
  

  145
  
  if (href === "")





  
  

  146
  
    href = "index.html";





  
  

  147
  
  var menuAnchor = $('a[href="' + href + '"]');





  
  

  148
  





  
  

  149
  
  // mark the anchor link active (and if it's in a dropdown, also mark that active)





  
  

  150
  
  var dropdown = menuAnchor.closest('li.dropdown');





  
  

  151
  
  if (window.bootstrap) { // Bootstrap 4+





  
  

  152
  
    menuAnchor.addClass('active');





  
  

  153
  
    dropdown.find('> .dropdown-toggle').addClass('active');





  
  

  154
  
  } else { // Bootstrap 3





  
  

  155
  
    menuAnchor.parent().addClass('active');





  
  

  156
  
    dropdown.addClass('active');





  
  

  157
  
  }





  
  

  158
  





  
  

  159
  
  // Navbar adjustments





  
  

  160
  
  var navHeight = $(".navbar").first().height() + 15;





  
  

  161
  
  var style = document.createElement('style');





  
  

  162
  
  var pt = "padding-top: " + navHeight + "px; ";





  
  

  163
  
  var mt = "margin-top: -" + navHeight + "px; ";





  
  

  164
  
  var css = "";





  
  

  165
  
  // offset scroll position for anchor links (for fixed navbar)





  
  

  166
  
  for (var i = 1; i <= 6; i++) {





  
  

  167
  
    css += ".section h" + i + "{ " + pt + mt + "}\n";





  
  

  168
  
  }





  
  

  169
  
  style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;





  
  

  170
  
  document.head.appendChild(style);





  
  

  171
  
});





  
  

  172
  
</script>





  
  

  173
  





  
  

  174
  
<!-- tabsets -->





  
  

  175
  





  
  

  176
  
<style type="text/css">





  
  

  177
  
.tabset-dropdown > .nav-tabs {





  
  

  178
  
  display: inline-table;





  
  

  179
  
  max-height: 500px;





  
  

  180
  
  min-height: 44px;





  
  

  181
  
  overflow-y: auto;





  
  

  182
  
  border: 1px solid #ddd;





  
  

  183
  
  border-radius: 4px;





  
  

  184
  
}





  
  

  185
  





  
  

  186
  
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {





  
  

  187
  
  content: "\e259";





  
  

  188
  
  font-family: 'Glyphicons Halflings';





  
  

  189
  
  display: inline-block;





  
  

  190
  
  padding: 10px;





  
  

  191
  
  border-right: 1px solid #ddd;





  
  

  192
  
}





  
  

  193
  





  
  

  194
  
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {





  
  

  195
  
  content: "\e258";





  
  

  196
  
  font-family: 'Glyphicons Halflings';





  
  

  197
  
  border: none;





  
  

  198
  
}





  
  

  199
  





  
  

  200
  
.tabset-dropdown > .nav-tabs > li.active {





  
  

  201
  
  display: block;





  
  

  202
  
}





  
  

  203
  





  
  

  204
  
.tabset-dropdown > .nav-tabs > li > a,





  
  

  205
  
.tabset-dropdown > .nav-tabs > li > a:focus,





  
  

  206
  
.tabset-dropdown > .nav-tabs > li > a:hover {





  
  

  207
  
  border: none;





  
  

  208
  
  display: inline-block;





  
  

  209
  
  border-radius: 4px;





  
  

  210
  
  background-color: transparent;





  
  

  211
  
}





  
  

  212
  





  
  

  213
  
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {





  
  

  214
  
  display: block;





  
  

  215
  
  float: none;





  
  

  216
  
}





  
  

  217
  





  
  

  218
  
.tabset-dropdown > .nav-tabs > li {





  
  

  219
  
  display: none;





  
  

  220
  
}





  
  

  221
  
</style>





  
  

  222
  





  
  

  223
  
<!-- code folding -->





  
  

  224
  





  
  

  225
  





  
  

  226
  





  
  

  227
  
<style type="text/css">





  
  

  228
  





  
  

  229
  
#TOC {





  
  

  230
  
  margin: 25px 0px 20px 0px;





  
  

  231
  
}





  
  

  232
  
@media (max-width: 768px) {





  
  

  233
  
#TOC {





  
  

  234
  
  position: relative;





  
  

  235
  
  width: 100%;





  
  

  236
  
}





  
  

  237
  
}





  
  

  238
  





  
  

  239
  
@media print {





  
  

  240
  
.toc-content {





  
  

  241
  
  /* see https://github.com/w3c/csswg-drafts/issues/4434 */





  
  

  242
  
  float: right;





  
  

  243
  
}





  
  

  244
  
}





  
  

  245
  





  
  

  246
  
.toc-content {





  
  

  247
  
  padding-left: 30px;





  
  

  248
  
  padding-right: 40px;





  
  

  249
  
}





  
  

  250
  





  
  

  251
  
div.main-container {





  
  

  252
  
  max-width: 1200px;





  
  

  253
  
}





  
  

  254
  





  
  

  255
  
div.tocify {





  
  

  256
  
  width: 20%;





  
  

  257
  
  max-width: 260px;





  
  

  258
  
  max-height: 85%;





  
  

  259
  
}





  
  

  260
  





  
  

  261
  
@media (min-width: 768px) and (max-width: 991px) {





  
  

  262
  
  div.tocify {





  
  

  263
  
    width: 25%;





  
  

  264
  
  }





  
  

  265
  
}





  
  

  266
  





  
  

  267
  
@media (max-width: 767px) {





  
  

  268
  
  div.tocify {





  
  

  269
  
    width: 100%;





  
  

  270
  
    max-width: none;





  
  

  271
  
  }





  
  

  272
  
}





  
  

  273
  





  
  

  274
  
.tocify ul, .tocify li {





  
  

  275
  
  line-height: 20px;





  
  

  276
  
}





  
  

  277
  





  
  

  278
  
.tocify-subheader .tocify-item {





  
  

  279
  
  font-size: 0.90em;





  
  

  280
  
}





  
  

  281
  





  
  

  282
  
.tocify .list-group-item {





  
  

  283
  
  border-radius: 0px;





  
  

  284
  
}





  
  

  285
  





  
  

  286
  
.tocify-subheader {





  
  

  287
  
  display: inline;





  
  

  288
  
}





  
  

  289
  
.tocify-subheader .tocify-item {





  
  

  290
  
  font-size: 0.95em;





  
  

  291
  
}





  
  

  292
  





  
  

  293
  
</style>





  
  

  294
  





  
  

  295
  





  
  

  296
  





  
  

  297
  
</head>





  
  

  298
  





  
  

  299
  
<body>





  
  

  300
  





  
  

  301
  





  
  

  302
  
<div class="container-fluid main-container">





  
  

  303
  





  
  

  304
  





  
  

  305
  
<!-- setup 3col/9col grid for toc_float and main content  -->





  
  

  306
  
<div class="row">





  
  

  307
  
<div class="col-xs-12 col-sm-4 col-md-3">





  
  

  308
  
<div id="TOC" class="tocify">





  
  

  309
  
</div>





  
  

  310
  
</div>





  
  

  311
  





  
  

  312
  
<div class="toc-content col-xs-12 col-sm-8 col-md-9">





  
  

  313
  





  
  

  314
  





  
  

  315
  





  
  

  316
  





  
  

  317
  
<div class="navbar navbar-default  navbar-fixed-top" role="navigation">





  
  

  318
  
  <div class="container">





  
  

  319
  
    <div class="navbar-header">





  
  

  320
  
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">





  
  

  321
  
        <span class="icon-bar"></span>





  
  

  322
  
        <span class="icon-bar"></span>





  
  

  323
  
        <span class="icon-bar"></span>





  
  

  324
  
      </button>





  
  

  325
  
      <a class="navbar-brand" href="index.html">VoltRon</a>





  
  

  326
  
    </div>





  
  

  327
  
    <div id="navbar" class="navbar-collapse collapse">





  
  

  328
  
      <ul class="nav navbar-nav">





  
  

  329
  
        <li>





  
  

  330
  
  <a href="tutorials.html">Explore</a>





  
  

  331
  
</li>





  
  

  332
  
<li class="dropdown">





  
  

  333
  
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

  334
  
    Vignette





  
  

  335
  
     





  
  

  336
  
    <span class="caret"></span>





  
  

  337
  
  </a>





  
  

  338
  
  <ul class="dropdown-menu" role="menu">





  
  

  339
  
    <li class="dropdown-submenu">





  
  

  340
  
      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Spatial Data Integration</a>





  
  

  341
  
      <ul class="dropdown-menu" role="menu">





  
  

  342
  
        <li>





  
  

  343
  
          <a href="registration.html">Spatial Data Alignment</a>





  
  

  344
  
        </li>





  
  

  345
  
        <li>





  
  

  346
  
          <a href="multiomic.html">Multi-omic Integration</a>





  
  

  347
  
        </li>





  
  

  348
  
        <li>





  
  

  349
  
          <a href="nicheclustering.html">Niche Clustering</a>





  
  

  350
  
        </li>





  
  

  351
  
      </ul>





  
  

  352
  
    </li>





  
  

  353
  
    <li class="dropdown-submenu">





  
  

  354
  
      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Downstream Analysis</a>





  
  

  355
  
      <ul class="dropdown-menu" role="menu">





  
  

  356
  
        <li>





  
  

  357
  
          <a href="roianalysis.html">ROI Analysis</a>





  
  

  358
  
        </li>





  
  

  359
  
        <li>





  
  

  360
  
          <a href="spotanalysis.html">Cell/Spot Analysis</a>





  
  

  361
  
        </li>





  
  

  362
  
        <li>





  
  

  363
  
          <a href="moleculeanalysis.html">Molecule Analysis</a>





  
  

  364
  
        </li>





  
  

  365
  
        <li>





  
  

  366
  
          <a href="pixelanalysis.html">Pixels (Image Only) Analysis</a>





  
  

  367
  
        </li>





  
  

  368
  
      </ul>





  
  

  369
  
    </li>





  
  

  370
  
    <li class="dropdown-submenu">





  
  

  371
  
      <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Utilities</a>





  
  

  372
  
      <ul class="dropdown-menu" role="menu">





  
  

  373
  
        <li>





  
  

  374
  
          <a href="interactive.html">Interactive Utilities</a>





  
  

  375
  
        </li>





  
  

  376
  
        <li>





  
  

  377
  
          <a href="importingdata.html">Importing Spatial Data</a>





  
  

  378
  
        </li>





  
  

  379
  
        <li>





  
  

  380
  
          <a href="voltronobjects.html">Working with VoltRon Objects</a>





  
  

  381
  
        </li>





  
  

  382
  
        <li>





  
  

  383
  
          <a href="conversion.html">Converting VoltRon Objects</a>





  
  

  384
  
        </li>





  
  

  385
  
        <li>





  
  

  386
  
          <a href="ondisk.html">OnDisk-based Analysis Utilities</a>





  
  

  387
  
        </li>





  
  

  388
  
      </ul>





  
  

  389
  
    </li>





  
  

  390
  
  </ul>





  
  

  391
  
</li>





  
  

  392
  
      </ul>





  
  

  393
  
      <ul class="nav navbar-nav navbar-right">





  
  

  394
  
        <li class="dropdown">





  
  

  395
  
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

  396
  
    <span class="fa fa-envelope-o"></span>





  
  

  397
  
     





  
  

  398
  
    Contact





  
  

  399
  
     





  
  

  400
  
    <span class="caret"></span>





  
  

  401
  
  </a>





  
  

  402
  
  <ul class="dropdown-menu" role="menu">





  
  

  403
  
    <li>





  
  

  404
  
      <a href="https://bioinformatics.mdc-berlin.de">Altuna Lab/BIMSB Bioinfo</a>





  
  

  405
  
    </li>





  
  

  406
  
    <li>





  
  

  407
  
      <a href="https://www.mdc-berlin.de/landthaler">Landthaler Lab/BIMSB</a>





  
  

  408
  
    </li>





  
  

  409
  
  </ul>





  
  

  410
  
</li>





  
  

  411
  
<li class="dropdown">





  
  

  412
  
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">





  
  

  413
  
    <span class="fa fa-github"></span>





  
  

  414
  
     





  
  

  415
  
    GitHub





  
  

  416
  
     





  
  

  417
  
    <span class="caret"></span>





  
  

  418
  
  </a>





  
  

  419
  
  <ul class="dropdown-menu" role="menu">





  
  

  420
  
    <li>





  
  

  421
  
      <a href="https://github.com/BIMSBbioinfo/VoltRon">VoltRon</a>





  
  

  422
  
    </li>





  
  

  423
  
    <li>





  
  

  424
  
      <a href="https://github.com/BIMSBbioinfo">BIMSB Bioinfo</a>





  
  

  425
  
    </li>





  
  

  426
  
  </ul>





  
  

  427
  
</li>





  
  

  428
  
      </ul>





  
  

  429
  
    </div><!--/.nav-collapse -->





  
  

  430
  
  </div><!--/.container -->





  
  

  431
  
</div><!--/.navbar -->





  
  

  432
  





  
  

  433
  
<div id="header">





  
  

  434
  





  
  

  435
  





  
  

  436
  





  
  

  437
  
<h1 class="title toc-ignore">ondisk</h1>





  
  

  438
  





  
  

  439
  
</div>





  
  

  440
  





  
  

  441
  





  
  

  442
  
<style>





  
  

  443
  
.title{





  
  

  444
  
  display: none;





  
  

  445
  
}





  
  

  446
  
body {





  
  

  447
  
  text-align: justify





  
  

  448
  
}





  
  

  449
  
.center {





  
  

  450
  
  display: block;





  
  

  451
  
  margin-left: auto;





  
  

  452
  
  margin-right: auto;





  
  

  453
  
}





  
  

  454
  
</style>





  
  

  455
  
<style type="text/css">





  
  

  456
  
.watch-out {





  
  

  457
  
  color: black;





  
  

  458
  
}





  
  

  459
  
</style>





  
  

  460
  
<p><br></p>





  
  

  461
  
<div id="import-visiumhd-data" class="section level2">





  
  

  462
  
<h2>Import VisiumHD Data</h2>





  
  

  463
  
<p>We first have to download some packages that are necessary to import





  
  

  464
  
datasets from <code>.parquet</code> and <code>.h5</code> files provided





  
  

  465
  
by the VisiumHD readouts.</p>





  
  

  466
  
<pre class="r watch-out"><code>install.packages(&quot;arrow&quot;)





  
  

  467
  
BiocManager::install(&quot;rhdf5&quot;)





  
  

  468
  
library(arrow)





  
  

  469
  
library(rhdf5)</code></pre>





  
  

  470
  
<p>We use the <strong>importVisiumHD</strong> function to start





  
  

  471
  
analyzing the data. The data has 393401 spots which we will use





  
  

  472
  
OnDisk-backed methods to efficiently manipulate, analyze and visualize





  
  

  473
  
these spots.</p>





  
  

  474
  
<p>The VisiumHD readouts provide multiple bin sizes which are aggregated





  
  

  475
  
versions of the original 2<span class="math inline">\(\mu\)</span>m





  
  

  476
  
<span class="math inline">\(x\)</span> 2<span





  
  

  477
  
class="math inline">\(\mu\)</span>m capture spots. The default bin sizes





  
  

  478
  
are <strong>(i)</strong> 2<span class="math inline">\(\mu\)</span>m





  
  

  479
  
<span class="math inline">\(x\)</span> 2<span





  
  

  480
  
class="math inline">\(\mu\)</span>m, <strong>(ii)</strong> 8<span





  
  

  481
  
class="math inline">\(\mu\)</span>m <span





  
  

  482
  
class="math inline">\(x\)</span> 8<span





  
  

  483
  
class="math inline">\(\mu\)</span>m and <strong>(iii)</strong> 16<span





  
  

  484
  
class="math inline">\(\mu\)</span>m <span





  
  

  485
  
class="math inline">\(x\)</span> 16<span





  
  

  486
  
class="math inline">\(\mu\)</span>m.</p>





  
  

  487
  
<pre class="r watch-out"><code>hddata &lt;- importVisiumHD(dir.path = &quot;VisiumHD/outs/&quot;, 





  
  

  488
  
                         bin.size = &quot;8&quot;, 





  
  

  489
  
                         resolution_level = &quot;hires&quot;)</code></pre>





  
  

  490
  
<p><br></p>





  
  

  491
  
</div>





  
  

  492
  
<div id="savingloading-voltron-objects" class="section level2">





  
  

  493
  
<h2>Saving/Loading VoltRon Objects</h2>





  
  

  494
  
<p>We use <strong>BPCells</strong> and <strong>ImageArray</strong>





  
  

  495
  
packages to accelerate operations of feature matrices and images. Here





  
  

  496
  
<strong>BPCells</strong> allows users access and operate on large





  
  

  497
  
feature matrices or clustering/spatial analysis, while





  
  

  498
  
<strong>ImageArray</strong> provides <a





  
  

  499
  
href="https://en.wikipedia.org/wiki/Pyramid_(image_processing)">pyramids





  
  

  500
  
images</a> to allow fast access to large microscopy images. You can





  
  

  501
  
download these package from GitHub using <strong>devtools</strong>.</p>





  
  

  502
  
<pre class="r watch-out"><code>devtools::install_github(&quot;bnprks/BPCells/r&quot;)





  
  

  503
  
devtools::install_github(&quot;BIMSBbioinfo/ImageArray&quot;)





  
  

  504
  
library(BPCells)





  
  

  505
  
library(ImageArray)</code></pre>





  
  

  506
  
<p>We can now save the VoltRon object to disk, large matrices and images





  
  

  507
  
will be written to either <strong>hdf5</strong> or <strong>zarr</strong>





  
  

  508
  
files depending on the <strong>format</strong> arguement, and the rest





  
  

  509
  
of the R object would be written to an <code>.rds</code> file, both





  
  

  510
  
under the designated <strong>output</strong>.</p>





  
  

  511
  
<pre class="r watch-out"><code>hddata &lt;- saveVoltRon(hddata, format = &quot;HDF5VoltRon&quot;, output = &quot;data/VisiumHD&quot;)</code></pre>





  
  

  512
  
<p>If you want you can load the VoltRon object from the same path as you





  
  

  513
  
have saved.</p>





  
  

  514
  
<pre class="r watch-out"><code>hddata &lt;- loadVoltRon(&quot;data/VisiumHD/&quot;)</code></pre>





  
  

  515
  
<p><br></p>





  
  

  516
  
</div>





  
  

  517
  
<div id="cellspot-analysis" class="section level2">





  
  

  518
  
<h2>Cell/Spot Analysis</h2>





  
  

  519
  
<p>The <strong>BPCells</strong> package provides fast methods to achieve





  
  

  520
  
operations common to single cell analysis such as filtering,





  
  

  521
  
normalization and dimensionality reduction. Here we have an example of





  
  

  522
  
single-cell like clustering of VisiumHD bins which is efficiently





  
  

  523
  
clustered.</p>





  
  

  524
  
<pre class="r watch-out"><code>spatialpoints &lt;- vrSpatialPoints(hddata)[as.vector(Metadata(hddata)$Count &gt; 10)]





  
  

  525
  
hddata &lt;- subset(hddata, spatialpoints = spatialpoints)





  
  

  526
  
hddata &lt;- normalizeData(hddata, sizefactor = 10000)





  
  

  527
  
hddata &lt;- getFeatures(hddata, n = 3000)





  
  

  528
  
selected_features &lt;- getVariableFeatures(hddata)





  
  

  529
  
hddata &lt;- getPCA(hddata, features = selected_features, dims = 30)





  
  

  530
  
hddata &lt;- getUMAP(hddata, dims = 1:30)</code></pre>





  
  

  531
  
<p>We can now visualized genes over embedding or spatial plots.</p>





  
  

  532
  
<pre class="r watch-out"><code>vrEmbeddingFeaturePlot(hddata, features = &quot;Nrgn&quot;, embedding = &quot;umap&quot;)





  
  

  533
  
vrSpatialFeaturePlot(hddata, features = &quot;Nrgn&quot;)</code></pre>





  
  

  534
  
<table>





  
  

  535
  
<tbody>





  
  

  536
  
<tr style="vertical-align: center">





  
  

  537
  
<td style="width:50%; vertical-align: center">





  
  

  538
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/ondisk_embeddingfeature.png" class="center">





  
  

  539
  
</td>





  
  

  540
  
<td style="width:55%; vertical-align: center">





  
  

  541
  
<img src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/ondisk_spatialfeature.png" class="center">





  
  

  542
  
</td>





  
  

  543
  
</tr>





  
  

  544
  
</tbody>





  
  

  545
  
</table>





  
  

  546
  
<p><br></p>





  
  

  547
  
</div>





  
  

  548
  
<div id="spatial-data-alignment" class="section level2">





  
  

  549
  
<h2>Spatial Data Alignment</h2>





  
  

  550
  
<p>The image registration workflow in the <a





  
  

  551
  
href="registration.html">Spatial Data Alignment</a> tutorial can also be





  
  

  552
  
conducted using disk-backed methods of the VoltRon package.</p>





  
  

  553
  
<pre class="r watch-out"><code>library(VoltRon)





  
  

  554
  
Xen_R1 &lt;- importXenium(&quot;Xenium_R1/outs&quot;, sample_name = &quot;XeniumR1&quot;, resolution_level = 3)





  
  

  555
  
Xen_R1_image &lt;- importImageData(&quot;Xenium_FFPE_Human_Breast_Cancer_Rep1_he_image.tif&quot;,





  
  

  556
  
                                sample_name = &quot;XeniumR1image&quot;,





  
  

  557
  
                                image_name = &quot;H&amp;E&quot;)</code></pre>





  
  

  558
  
<p><br></p>





  
  

  559
  
<p>We can save both Xenium and H&amp;E (image) datasets to disk before





  
  

  560
  
using the mini Shiny app for registration</p>





  
  

  561
  
<pre class="r watch-out"><code>Xen_R1_disk &lt;- saveVoltRon(Xen_R1, 





  
  

  562
  
                           format = &quot;HDF5VoltRon&quot;, 





  
  

  563
  
                           output = &quot;data/Xen_R1_h5&quot;, replace = TRUE)





  
  

  564
  
Xen_R1_image_disk &lt;- saveVoltRon(Xen_R1_image,





  
  

  565
  
                                 format = &quot;HDF5VoltRon&quot;, 





  
  

  566
  
                                 output = &quot;data/Xen_R1_image_h5&quot;, replace = TRUE)</code></pre>





  
  

  567
  
<p><br></p>





  
  

  568
  
<p>These disk-based datasets can then be loaded from the disk





  
  

  569
  
easily.</p>





  
  

  570
  
<pre class="r watch-out"><code>Xen_R1_disk &lt;- loadVoltRon(&quot;../data/OnDisk/Xen_R1_h5/&quot;)





  
  

  571
  
Xen_R1_image_disk &lt;- loadVoltRon(&quot;../data/OnDisk/Xen_R1_image_h5/&quot;)</code></pre>





  
  

  572
  
<p><br></p>





  
  

  573
  
<p>VoltRon stores large images as pyramids to increase interactive





  
  

  574
  
visualization efficiency. This storage strategy allows shiny apps to





  
  

  575
  
zoom in to tissue niches in a speedy fashion. VoltRon incorporates





  
  

  576
  
<code>Image_Array</code> objects (<a





  
  

  577
  
href="https://github.com/BIMSBbioinfo/ImageArray"





  
  

  578
  
class="uri">https://github.com/BIMSBbioinfo/ImageArray</a>) to define





  
  

  579
  
these pyramids.</p>





  
  

  580
  
<pre class="r watch-out"><code>vrImages(Xen_R1_image_disk, as.raster = TRUE)</code></pre>





  
  

  581
  
<pre><code>Image_Array Object 





  
  

  582
  
Series 1 of size (3,27587,20511) 





  
  

  583
  
Series 2 of size (3,13794,10256) 





  
  

  584
  
Series 3 of size (3,6897,5128) 





  
  

  585
  
Series 4 of size (3,3449,2564) 





  
  

  586
  
Series 5 of size (3,1725,1282) 





  
  

  587
  
Series 6 of size (3,863,641) 





  
  

  588
  
Series 7 of size (3,432,321) </code></pre>





  
  

  589
  
<p><br></p>





  
  

  590
  
<p>We can now visualize and align the Xenium and H&amp;E objects.</p>





  
  

  591
  
<pre class="r watch-out"><code># Align spatial data





  
  

  592
  
xen_reg &lt;- registerSpatialData(object_list = list(Xen_R1_disk, Xen_R1_image_disk))</code></pre>





  
  

  593
  
<div>





  
  

  594
  
<p><video width="100%" height="100%" controls autoplay>





  
  

  595
  
<source src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/video_temp.mov" type="video/mp4">





  
  

  596
  
Your browser does not support the video tag. </video></p>





  
  

  597
  
</div>





  
  

  598
  
<p><br></p>





  
  

  599
  
<pre class="r watch-out"><code># transfer aligned H&amp;E to Xenium data





  
  

  600
  
Xenium_reg &lt;- xen_reg$registered_spat[[2]]





  
  

  601
  
vrImages(Xen_R1_disk[[&quot;Assay1&quot;]], name = &quot;main&quot;, channel = &quot;H&amp;E&quot;) &lt;- vrImages(Xenium_reg, name = &quot;H&amp;E_reg&quot;)





  
  

  602
  





  
  

  603
  
# visualize





  
  

  604
  
vrImages(Xen_R1_disk, channel = &quot;H&amp;E&quot;, scale.perc = 10)</code></pre>





  
  

  605
  
<p><br></p>





  
  

  606
  
<p><img width="92%" height="92%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/ondisk_alignedHE.png" class="center"></p>





  
  

  607
  
</div>





  
  

  608
  





  
  

  609
  





  
  

  610
  





  
  

  611
  
</div>





  
  

  612
  
</div>





  
  

  613
  





  
  

  614
  
</div>





  
  

  615
  





  
  

  616
  
<script>





  
  

  617
  





  
  

  618
  
// add bootstrap table styles to pandoc tables





  
  

  619
  
function bootstrapStylePandocTables() {





  
  

  620
  
  $('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');





  
  

  621
  
}





  
  

  622
  
$(document).ready(function () {





  
  

  623
  
  bootstrapStylePandocTables();





  
  

  624
  
});





  
  

  625
  





  
  

  626
  





  
  

  627
  
</script>





  
  

  628
  





  
  

  629
  
<!-- tabsets -->





  
  

  630
  





  
  

  631
  
<script>





  
  

  632
  
$(document).ready(function () {





  
  

  633
  
  window.buildTabsets("TOC");





  
  

  634
  
});





  
  

  635
  





  
  

  636
  
$(document).ready(function () {





  
  

  637
  
  $('.tabset-dropdown > .nav-tabs > li').click(function () {





  
  

  638
  
    $(this).parent().toggleClass('nav-tabs-open');





  
  

  639
  
  });





  
  

  640
  
});





  
  

  641
  
</script>





  
  

  642
  





  
  

  643
  
<!-- code folding -->





  
  

  644
  





  
  

  645
  
<script>





  
  

  646
  
$(document).ready(function ()  {





  
  

  647
  





  
  

  648
  
    // temporarily add toc-ignore selector to headers for the consistency with Pandoc





  
  

  649
  
    $('.unlisted.unnumbered').addClass('toc-ignore')





  
  

  650
  





  
  

  651
  
    // move toc-ignore selectors from section div to header





  
  

  652
  
    $('div.section.toc-ignore')





  
  

  653
  
        .removeClass('toc-ignore')





  
  

  654
  
        .children('h1,h2,h3,h4,h5').addClass('toc-ignore');





  
  

  655
  





  
  

  656
  
    // establish options





  
  

  657
  
    var options = {





  
  

  658
  
      selectors: "h1,h2,h3",





  
  

  659
  
      theme: "bootstrap3",





  
  

  660
  
      context: '.toc-content',





  
  

  661
  
      hashGenerator: function (text) {





  
  

  662
  
        return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');





  
  

  663
  
      },





  
  

  664
  
      ignoreSelector: ".toc-ignore",





  
  

  665
  
      scrollTo: 0





  
  

  666
  
    };





  
  

  667
  
    options.showAndHide = false;





  
  

  668
  
    options.smoothScroll = false;





  
  

  669
  





  
  

  670
  
    // tocify





  
  

  671
  
    var toc = $("#TOC").tocify(options).data("toc-tocify");





  
  

  672
  
});





  
  

  673
  
</script>





  
  

  674
  





  
  

  675
  
<!-- dynamically load mathjax for compatibility with self-contained -->





  
  

  676
  
<script>





  
  

  677
  
  (function () {





  
  

  678
  
    var script = document.createElement("script");





  
  

  679
  
    script.type = "text/javascript";





  
  

  680
  
    script.src  = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";





  
  

  681
  
    document.getElementsByTagName("head")[0].appendChild(script);





  
  

  682
  
  })();





  
  

  683
  
</script>





  
  

  684
  





  
  

  685
  
</body>





  
  

  686
  
</html>