Skip to content

Commit 767be7f

Browse files
author
Sean Wilson
committed
updated graphic and vignette
1 parent baae41c commit 767be7f

File tree

2 files changed

+337
-0
lines changed

2 files changed

+337
-0
lines changed

‎Model_Graphic.png

1.32 MB
Loading

‎vignettes/DevKidCC.html

Lines changed: 337 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,337 @@
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+
<meta name="viewport" content="width=device-width, initial-scale=1" />
12+
13+
14+
15+
<title>DevKidCC</title>
16+
17+
18+
19+
<style type="text/css">code{white-space: pre;}</style>
20+
<style type="text/css" data-origin="pandoc">
21+
a.sourceLine { display: inline-block; line-height: 1.25; }
22+
a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
23+
a.sourceLine:empty { height: 1.2em; }
24+
.sourceCode { overflow: visible; }
25+
code.sourceCode { white-space: pre; position: relative; }
26+
div.sourceCode { margin: 1em 0; }
27+
pre.sourceCode { margin: 0; }
28+
@media screen {
29+
div.sourceCode { overflow: auto; }
30+
}
31+
@media print {
32+
code.sourceCode { white-space: pre-wrap; }
33+
a.sourceLine { text-indent: -1em; padding-left: 1em; }
34+
}
35+
pre.numberSource a.sourceLine
36+
{ position: relative; left: -4em; }
37+
pre.numberSource a.sourceLine::before
38+
{ content: attr(data-line-number);
39+
position: relative; left: -1em; text-align: right; vertical-align: baseline;
40+
border: none; pointer-events: all; display: inline-block;
41+
-webkit-touch-callout: none; -webkit-user-select: none;
42+
-khtml-user-select: none; -moz-user-select: none;
43+
-ms-user-select: none; user-select: none;
44+
padding: 0 4px; width: 4em;
45+
color: #aaaaaa;
46+
}
47+
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
48+
div.sourceCode
49+
{ }
50+
@media screen {
51+
a.sourceLine::before { text-decoration: underline; }
52+
}
53+
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
54+
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
55+
code span.at { color: #7d9029; } /* Attribute */
56+
code span.bn { color: #40a070; } /* BaseN */
57+
code span.bu { } /* BuiltIn */
58+
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
59+
code span.ch { color: #4070a0; } /* Char */
60+
code span.cn { color: #880000; } /* Constant */
61+
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
62+
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
63+
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
64+
code span.dt { color: #902000; } /* DataType */
65+
code span.dv { color: #40a070; } /* DecVal */
66+
code span.er { color: #ff0000; font-weight: bold; } /* Error */
67+
code span.ex { } /* Extension */
68+
code span.fl { color: #40a070; } /* Float */
69+
code span.fu { color: #06287e; } /* Function */
70+
code span.im { } /* Import */
71+
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
72+
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
73+
code span.op { color: #666666; } /* Operator */
74+
code span.ot { color: #007020; } /* Other */
75+
code span.pp { color: #bc7a00; } /* Preprocessor */
76+
code span.sc { color: #4070a0; } /* SpecialChar */
77+
code span.ss { color: #bb6688; } /* SpecialString */
78+
code span.st { color: #4070a0; } /* String */
79+
code span.va { color: #19177c; } /* Variable */
80+
code span.vs { color: #4070a0; } /* VerbatimString */
81+
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
82+
83+
</style>
84+
<script>
85+
// apply pandoc div.sourceCode style to pre.sourceCode instead
86+
(function() {
87+
var sheets = document.styleSheets;
88+
for (var i = 0; i < sheets.length; i++) {
89+
if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
90+
try { var rules = sheets[i].cssRules; } catch (e) { continue; }
91+
for (var j = 0; j < rules.length; j++) {
92+
var rule = rules[j];
93+
// check if there is a div.sourceCode rule
94+
if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") continue;
95+
var style = rule.style.cssText;
96+
// check if color or background-color is set
97+
if (rule.style.color === '' && rule.style.backgroundColor === '') continue;
98+
// replace div.sourceCode by a pre.sourceCode rule
99+
sheets[i].deleteRule(j);
100+
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
101+
}
102+
}
103+
})();
104+
</script>
105+
106+
107+
108+
<style type="text/css">body {
109+
background-color: #fff;
110+
margin: 1em auto;
111+
max-width: 700px;
112+
overflow: visible;
113+
padding-left: 2em;
114+
padding-right: 2em;
115+
font-family: "Open Sans", "Helvetica Neue", Helvetica, Arial, sans-serif;
116+
font-size: 14px;
117+
line-height: 1.35;
118+
}
119+
#TOC {
120+
clear: both;
121+
margin: 0 0 10px 10px;
122+
padding: 4px;
123+
width: 400px;
124+
border: 1px solid #CCCCCC;
125+
border-radius: 5px;
126+
background-color: #f6f6f6;
127+
font-size: 13px;
128+
line-height: 1.3;
129+
}
130+
#TOC .toctitle {
131+
font-weight: bold;
132+
font-size: 15px;
133+
margin-left: 5px;
134+
}
135+
#TOC ul {
136+
padding-left: 40px;
137+
margin-left: -1.5em;
138+
margin-top: 5px;
139+
margin-bottom: 5px;
140+
}
141+
#TOC ul ul {
142+
margin-left: -2em;
143+
}
144+
#TOC li {
145+
line-height: 16px;
146+
}
147+
table {
148+
margin: 1em auto;
149+
border-width: 1px;
150+
border-color: #DDDDDD;
151+
border-style: outset;
152+
border-collapse: collapse;
153+
}
154+
table th {
155+
border-width: 2px;
156+
padding: 5px;
157+
border-style: inset;
158+
}
159+
table td {
160+
border-width: 1px;
161+
border-style: inset;
162+
line-height: 18px;
163+
padding: 5px 5px;
164+
}
165+
table, table th, table td {
166+
border-left-style: none;
167+
border-right-style: none;
168+
}
169+
table thead, table tr.even {
170+
background-color: #f7f7f7;
171+
}
172+
p {
173+
margin: 0.5em 0;
174+
}
175+
blockquote {
176+
background-color: #f6f6f6;
177+
padding: 0.25em 0.75em;
178+
}
179+
hr {
180+
border-style: solid;
181+
border: none;
182+
border-top: 1px solid #777;
183+
margin: 28px 0;
184+
}
185+
dl {
186+
margin-left: 0;
187+
}
188+
dl dd {
189+
margin-bottom: 13px;
190+
margin-left: 13px;
191+
}
192+
dl dt {
193+
font-weight: bold;
194+
}
195+
ul {
196+
margin-top: 0;
197+
}
198+
ul li {
199+
list-style: circle outside;
200+
}
201+
ul ul {
202+
margin-bottom: 0;
203+
}
204+
pre, code {
205+
background-color: #f7f7f7;
206+
border-radius: 3px;
207+
color: #333;
208+
white-space: pre-wrap;
209+
}
210+
pre {
211+
border-radius: 3px;
212+
margin: 5px 0px 10px 0px;
213+
padding: 10px;
214+
}
215+
pre:not([class]) {
216+
background-color: #f7f7f7;
217+
}
218+
code {
219+
font-family: Consolas, Monaco, 'Courier New', monospace;
220+
font-size: 85%;
221+
}
222+
p > code, li > code {
223+
padding: 2px 0px;
224+
}
225+
div.figure {
226+
text-align: center;
227+
}
228+
img {
229+
background-color: #FFFFFF;
230+
padding: 2px;
231+
border: 1px solid #DDDDDD;
232+
border-radius: 3px;
233+
border: 1px solid #CCCCCC;
234+
margin: 0 5px;
235+
}
236+
h1 {
237+
margin-top: 0;
238+
font-size: 35px;
239+
line-height: 40px;
240+
}
241+
h2 {
242+
border-bottom: 4px solid #f7f7f7;
243+
padding-top: 10px;
244+
padding-bottom: 2px;
245+
font-size: 145%;
246+
}
247+
h3 {
248+
border-bottom: 2px solid #f7f7f7;
249+
padding-top: 10px;
250+
font-size: 120%;
251+
}
252+
h4 {
253+
border-bottom: 1px solid #f7f7f7;
254+
margin-left: 8px;
255+
font-size: 105%;
256+
}
257+
h5, h6 {
258+
border-bottom: 1px solid #ccc;
259+
font-size: 105%;
260+
}
261+
a {
262+
color: #0033dd;
263+
text-decoration: none;
264+
}
265+
a:hover {
266+
color: #6666ff; }
267+
a:visited {
268+
color: #800080; }
269+
a:visited:hover {
270+
color: #BB00BB; }
271+
a[href^="http:"] {
272+
text-decoration: underline; }
273+
a[href^="https:"] {
274+
text-decoration: underline; }
275+
276+
code > span.kw { color: #555; font-weight: bold; }
277+
code > span.dt { color: #902000; }
278+
code > span.dv { color: #40a070; }
279+
code > span.bn { color: #d14; }
280+
code > span.fl { color: #d14; }
281+
code > span.ch { color: #d14; }
282+
code > span.st { color: #d14; }
283+
code > span.co { color: #888888; font-style: italic; }
284+
code > span.ot { color: #007020; }
285+
code > span.al { color: #ff0000; font-weight: bold; }
286+
code > span.fu { color: #900; font-weight: bold; }
287+
code > span.er { color: #a61717; background-color: #e3d2d2; }
288+
</style>
289+
290+
291+
292+
293+
</head>
294+
295+
<body>
296+
297+
298+
299+
300+
<h1 class="title toc-ignore">DevKidCC</h1>
301+
302+
303+
304+
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(DevKidCC)</a>
305+
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">library</span>(tidyverse)</a></code></pre></div>
306+
<div id="introduction" class="section level1">
307+
<h1>Introduction</h1>
308+
<p>In this vignette I’ll run through how to use DevKidCC to classify kidney cells in scRNA-Seq data. I’ll then highlight the various visualisation tools that are included in the package.<br> <br></p>
309+
<div id="devkidcc" class="section level2">
310+
<h2>DevKidCC</h2>
311+
<p>First we need to load the data and generate a Seurat object. To generate a Seurat object from raw files, follow the tutorials at the <a href="https://satijalab.org/seurat/articles/pbmc3k_tutorial.html">Satija Lab website</a><br> <br> Here we will load the organoid dataset included with the package, from <a href>Howden et al. 2019</a></p>
312+
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw">load</span>(<span class="st">&quot;/group/kidn1/Group-Little_MCRI/People/Sean/PhD/R-projects/DevKidCC/data/organoid.rda&quot;</span>)</a>
313+
<a class="sourceLine" id="cb2-2" data-line-number="2">organoid</a>
314+
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="co">#&gt; An object of class Seurat </span></a>
315+
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">#&gt; 2000 features across 5365 samples within 1 assay </span></a>
316+
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co">#&gt; Active assay: RNA (2000 features, 2000 variable features)</span></a>
317+
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co">#&gt; 5 dimensional reductions calculated: cca, cca.aligned, tsne, pca, umap</span></a></code></pre></div>
318+
</div>
319+
</div>
320+
321+
322+
323+
<!-- code folding -->
324+
325+
326+
<!-- dynamically load mathjax for compatibility with self-contained -->
327+
<script>
328+
(function () {
329+
var script = document.createElement("script");
330+
script.type = "text/javascript";
331+
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
332+
document.getElementsByTagName("head")[0].appendChild(script);
333+
})();
334+
</script>
335+
336+
</body>
337+
</html>

0 commit comments

Comments
 (0)