-
Notifications
You must be signed in to change notification settings - Fork 2
/
README.html
640 lines (591 loc) · 23.4 KB
/
README.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>birch-beer</title>
<meta name="generator" content="Org mode" />
<meta name="author" content="Gregory W. Schwartz" />
<style type="text/css">
<!--/*--><![CDATA[/*><!--*/
.title { text-align: center;
margin-bottom: .2em; }
.subtitle { text-align: center;
font-size: medium;
font-weight: bold;
margin-top:0; }
.todo { font-family: monospace; color: red; }
.done { font-family: monospace; color: green; }
.priority { font-family: monospace; color: orange; }
.tag { background-color: #eee; font-family: monospace;
padding: 2px; font-size: 80%; font-weight: normal; }
.timestamp { color: #bebebe; }
.timestamp-kwd { color: #5f9ea0; }
.org-right { margin-left: auto; margin-right: 0px; text-align: right; }
.org-left { margin-left: 0px; margin-right: auto; text-align: left; }
.org-center { margin-left: auto; margin-right: auto; text-align: center; }
.underline { text-decoration: underline; }
#postamble p, #preamble p { font-size: 90%; margin: .2em; }
p.verse { margin-left: 3%; }
pre {
border: 1px solid #ccc;
box-shadow: 3px 3px 3px #eee;
padding: 8pt;
font-family: monospace;
overflow: auto;
margin: 1.2em;
}
pre.src {
position: relative;
overflow: auto;
padding-top: 1.2em;
}
pre.src:before {
display: none;
position: absolute;
background-color: white;
top: -10px;
right: 10px;
padding: 3px;
border: 1px solid black;
}
pre.src:hover:before { display: inline; margin-top: 14px;}
/* Languages per Org manual */
pre.src-asymptote:before { content: 'Asymptote'; }
pre.src-awk:before { content: 'Awk'; }
pre.src-C:before { content: 'C'; }
/* pre.src-C++ doesn't work in CSS */
pre.src-clojure:before { content: 'Clojure'; }
pre.src-css:before { content: 'CSS'; }
pre.src-D:before { content: 'D'; }
pre.src-ditaa:before { content: 'ditaa'; }
pre.src-dot:before { content: 'Graphviz'; }
pre.src-calc:before { content: 'Emacs Calc'; }
pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
pre.src-fortran:before { content: 'Fortran'; }
pre.src-gnuplot:before { content: 'gnuplot'; }
pre.src-haskell:before { content: 'Haskell'; }
pre.src-hledger:before { content: 'hledger'; }
pre.src-java:before { content: 'Java'; }
pre.src-js:before { content: 'Javascript'; }
pre.src-latex:before { content: 'LaTeX'; }
pre.src-ledger:before { content: 'Ledger'; }
pre.src-lisp:before { content: 'Lisp'; }
pre.src-lilypond:before { content: 'Lilypond'; }
pre.src-lua:before { content: 'Lua'; }
pre.src-matlab:before { content: 'MATLAB'; }
pre.src-mscgen:before { content: 'Mscgen'; }
pre.src-ocaml:before { content: 'Objective Caml'; }
pre.src-octave:before { content: 'Octave'; }
pre.src-org:before { content: 'Org mode'; }
pre.src-oz:before { content: 'OZ'; }
pre.src-plantuml:before { content: 'Plantuml'; }
pre.src-processing:before { content: 'Processing.js'; }
pre.src-python:before { content: 'Python'; }
pre.src-R:before { content: 'R'; }
pre.src-ruby:before { content: 'Ruby'; }
pre.src-sass:before { content: 'Sass'; }
pre.src-scheme:before { content: 'Scheme'; }
pre.src-screen:before { content: 'Gnu Screen'; }
pre.src-sed:before { content: 'Sed'; }
pre.src-sh:before { content: 'shell'; }
pre.src-sql:before { content: 'SQL'; }
pre.src-sqlite:before { content: 'SQLite'; }
/* additional languages in org.el's org-babel-load-languages alist */
pre.src-forth:before { content: 'Forth'; }
pre.src-io:before { content: 'IO'; }
pre.src-J:before { content: 'J'; }
pre.src-makefile:before { content: 'Makefile'; }
pre.src-maxima:before { content: 'Maxima'; }
pre.src-perl:before { content: 'Perl'; }
pre.src-picolisp:before { content: 'Pico Lisp'; }
pre.src-scala:before { content: 'Scala'; }
pre.src-shell:before { content: 'Shell Script'; }
pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
/* additional language identifiers per "defun org-babel-execute"
in ob-*.el */
pre.src-cpp:before { content: 'C++'; }
pre.src-abc:before { content: 'ABC'; }
pre.src-coq:before { content: 'Coq'; }
pre.src-groovy:before { content: 'Groovy'; }
/* additional language identifiers from org-babel-shell-names in
ob-shell.el: ob-shell is the only babel language using a lambda to put
the execution function name together. */
pre.src-bash:before { content: 'bash'; }
pre.src-csh:before { content: 'csh'; }
pre.src-ash:before { content: 'ash'; }
pre.src-dash:before { content: 'dash'; }
pre.src-ksh:before { content: 'ksh'; }
pre.src-mksh:before { content: 'mksh'; }
pre.src-posh:before { content: 'posh'; }
/* Additional Emacs modes also supported by the LaTeX listings package */
pre.src-ada:before { content: 'Ada'; }
pre.src-asm:before { content: 'Assembler'; }
pre.src-caml:before { content: 'Caml'; }
pre.src-delphi:before { content: 'Delphi'; }
pre.src-html:before { content: 'HTML'; }
pre.src-idl:before { content: 'IDL'; }
pre.src-mercury:before { content: 'Mercury'; }
pre.src-metapost:before { content: 'MetaPost'; }
pre.src-modula-2:before { content: 'Modula-2'; }
pre.src-pascal:before { content: 'Pascal'; }
pre.src-ps:before { content: 'PostScript'; }
pre.src-prolog:before { content: 'Prolog'; }
pre.src-simula:before { content: 'Simula'; }
pre.src-tcl:before { content: 'tcl'; }
pre.src-tex:before { content: 'TeX'; }
pre.src-plain-tex:before { content: 'Plain TeX'; }
pre.src-verilog:before { content: 'Verilog'; }
pre.src-vhdl:before { content: 'VHDL'; }
pre.src-xml:before { content: 'XML'; }
pre.src-nxml:before { content: 'XML'; }
/* add a generic configuration mode; LaTeX export needs an additional
(add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
pre.src-conf:before { content: 'Configuration File'; }
table { border-collapse:collapse; }
caption.t-above { caption-side: top; }
caption.t-bottom { caption-side: bottom; }
td, th { vertical-align:top; }
th.org-right { text-align: center; }
th.org-left { text-align: center; }
th.org-center { text-align: center; }
td.org-right { text-align: right; }
td.org-left { text-align: left; }
td.org-center { text-align: center; }
dt { font-weight: bold; }
.footpara { display: inline; }
.footdef { margin-bottom: 1em; }
.figure { padding: 1em; }
.figure p { text-align: center; }
.equation-container {
display: table;
text-align: center;
width: 100%;
}
.equation {
vertical-align: middle;
}
.equation-label {
display: table-cell;
text-align: right;
vertical-align: middle;
}
.inlinetask {
padding: 10px;
border: 2px solid gray;
margin: 10px;
background: #ffffcc;
}
#org-div-home-and-up
{ text-align: right; font-size: 70%; white-space: nowrap; }
textarea { overflow-x: auto; }
.linenr { font-size: smaller }
.code-highlighted { background-color: #ffff00; }
.org-info-js_info-navigation { border-style: none; }
#org-info-js_console-label
{ font-size: 10px; font-weight: bold; white-space: nowrap; }
.org-info-js_search-highlight
{ background-color: #ffff00; color: #000000; font-weight: bold; }
.org-svg { width: 90%; }
/*]]>*/-->
</style>
<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/htmlize.css"/>
<link rel="stylesheet" type="text/css" href="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/css/readtheorg.css"/>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/lib/js/jquery.stickytableheaders.min.js"></script>
<script type="text/javascript" src="https://fniessen.github.io/org-html-themes/src/readtheorg_theme/js/readtheorg.js"></script>
<script type="text/javascript">
// @license magnet:?xt=urn:btih:e95b018ef3580986a04669f1b5879592219e2a7a&dn=public-domain.txt Public Domain
<!--/*--><![CDATA[/*><!--*/
function CodeHighlightOn(elem, id)
{
var target = document.getElementById(id);
if(null != target) {
elem.classList.add("code-highlighted");
target.classList.add("code-highlighted");
}
}
function CodeHighlightOff(elem, id)
{
var target = document.getElementById(id);
if(null != target) {
elem.classList.remove("code-highlighted");
target.classList.remove("code-highlighted");
}
}
/*]]>*///-->
// @license-end
</script>
</head>
<body>
<div id="content">
<h1 class="title">birch-beer</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgb2401ab">Description</a></li>
<li><a href="#org13e194b">Installation</a>
<ul>
<li><a href="#orgb46a304">Use <code>nix</code></a></li>
<li><a href="#org204682d">Dependencies</a></li>
<li><a href="#org130b38e">Install <code>stack</code></a></li>
<li><a href="#org69ff251">Install <code>birch-beer</code></a>
<ul>
<li><a href="#org69b0f3c">Source</a></li>
<li><a href="#orgd99969a">Online</a></li>
<li><a href="#org07fbfab">Docker</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org7da20b4">Usage</a>
<ul>
<li><a href="#org20af828">Tree format</a>
<ul>
<li><a href="#org471f2dc">Example conversion from R</a></li>
</ul>
</li>
<li><a href="#orgf00c8d8">Labels format</a></li>
</ul>
</li>
<li><a href="#org56730ad">Select examples</a>
<ul>
<li><a href="#org138221b">Large tree</a></li>
<li><a href="#org4c2efa2">Number overlay</a></li>
<li><a href="#org7b1494c">Distance overlay</a></li>
<li><a href="#org0d7221d">Continuous color saturation</a></li>
<li><a href="#orgb7a229c">Continuous multi-color saturation</a></li>
<li><a href="#org51ecb12">Diversity of labels</a></li>
</ul>
</li>
</ul>
</div>
</div>
<p>
<a href="https://gregoryschwartz.github.io/birch-beer/">Website</a>
</p>
<p>
See <a href="https://github.com/GregorySchwartz/birch-beer">https://github.com/GregorySchwartz/birch-beer</a> for latest version.
</p>
<div id="outline-container-orgb2401ab" class="outline-2">
<h2 id="orgb2401ab">Description</h2>
<div class="outline-text-2" id="text-orgb2401ab">
<div id="orgacb21bd" class="figure">
<p><img src="img/piechart_pruned_tree.png" alt="piechart_pruned_tree.png" />
</p>
</div>
<p>
<code>birch-beer</code> is all about sweet trees. That is, visualizing hierarchical
structures where the elements are stored in leaves and parent nodes represent
all of the descendant leaves. Using branch scaling, weighted average color
blending, distance markers, and more, we can all create some home brewed
<code>birch-beer</code> together!
</p>
</div>
</div>
<div id="outline-container-org13e194b" class="outline-2">
<h2 id="org13e194b">Installation</h2>
<div class="outline-text-2" id="text-org13e194b">
</div>
<div id="outline-container-orgb46a304" class="outline-3">
<h3 id="orgb46a304">Use <code>nix</code></h3>
<div class="outline-text-3" id="text-orgb46a304">
<p>
Installing <code>birch-beer</code> using <code>nix</code> is the easiest way to install from source.
First, install <code>nix</code> following the instructions
<a href="https://nixos.org/nix/">on the website</a>. Then run the commands:
</p>
<div class="org-src-container">
<pre class="src src-sh">git clone https://github.com/GregorySchwartz/birch-beer.git
<span style="color: #ff8700;">cd</span> birch-beer
nix-env -f default.nix -i birch-beer
</pre>
</div>
<p>
Then the <code>birch-beer</code> command should be in your path! If you do not wish to use
<code>nix</code> or <code>docker</code>, then you can continue reading for dependencies and <code>stack</code>
installation (no longer supported).
</p>
</div>
</div>
<div id="outline-container-org204682d" class="outline-3">
<h3 id="org204682d">Dependencies</h3>
<div class="outline-text-3" id="text-org204682d">
<p>
You may require the following dependencies to build and run (from Ubuntu 16.04,
use the appropriate packages from your distribution of choice):
</p>
<ul class="org-ul">
<li>build-essential</li>
<li>libgmp-dev</li>
<li>libblas-dev</li>
<li>liblapack-dev</li>
<li>libgsl-dev</li>
<li>libgtk2.0-dev</li>
<li>libcairo2-dev</li>
<li>libpango1.0-dev</li>
<li>graphviz</li>
</ul>
</div>
</div>
<div id="outline-container-org130b38e" class="outline-3">
<h3 id="org130b38e">Install <code>stack</code></h3>
<div class="outline-text-3" id="text-org130b38e">
<p>
See <a href="https://docs.haskellstack.org/en/stable/README/">https://docs.haskellstack.org/en/stable/README/</a> for more details.
</p>
<div class="org-src-container">
<pre class="src src-sh">curl -sSL https://get.haskellstack.org/ | sh
stack setup
</pre>
</div>
</div>
</div>
<div id="outline-container-org69ff251" class="outline-3">
<h3 id="org69ff251">Install <code>birch-beer</code></h3>
<div class="outline-text-3" id="text-org69ff251">
</div>
<div id="outline-container-org69b0f3c" class="outline-4">
<h4 id="org69b0f3c">Source</h4>
<div class="outline-text-4" id="text-org69b0f3c">
<p>
Probably the easiest method if you don't want to mess with dependencies (outside
of the ones above).
</p>
<div class="org-src-container">
<pre class="src src-sh">git clone https://github.com/GregorySchwartz/birch-beer.git
<span style="color: #ff8700;">cd</span> birch-beer
stack install
</pre>
</div>
</div>
</div>
<div id="outline-container-orgd99969a" class="outline-4">
<h4 id="orgd99969a">Online</h4>
<div class="outline-text-4" id="text-orgd99969a">
<p>
We only require <code>stack</code> (or <code>cabal</code>), you do not need to download any source
code (but you might need the stack.yaml dependency versions), just run the
following command to place <code>birch-beer</code> in your <code>~/.local/bin/</code>:
</p>
<div class="org-src-container">
<pre class="src src-sh">stack install birch-beer
</pre>
</div>
<p>
If you run into errors like <code>Error: While constructing the build plan, the
following exceptions were encountered:</code>, then follow it's advice. Usually you
just need to follow the suggestion and add the dependencies to the specified
file. For a quick <code>yaml</code> configuration, refer to
<a href="https://github.com/GregorySchwartz/birch-beer/blob/master/stack.yaml">https://github.com/GregorySchwartz/birch-beer/blob/master/stack.yaml</a>. Relies on
<code>eigen-3.3.4.1</code> right now.
</p>
</div>
</div>
<div id="outline-container-org07fbfab" class="outline-4">
<h4 id="org07fbfab">Docker</h4>
<div class="outline-text-4" id="text-org07fbfab">
<p>
Different computers have different setups, operating systems, and repositories.
Do put the entire program in a container to bypass difficulties (with the other
methods above), we user <code>docker</code>. So first, <a href="https://docs.docker.com/">install docker</a>.
</p>
<p>
To get <code>birch-beer</code> (replace 0.1.0.0 with <a href="https://cloud.docker.com/repository/docker/gregoryschwartz/birch-beer/general">any version needed</a>):
</p>
<div class="org-src-container">
<pre class="src src-sh">docker pull gregoryschwartz/birch-beer:0.1.0.0
</pre>
</div>
<p>
To run <code>birch-beer</code> in a docker container:
</p>
<div class="org-src-container">
<pre class="src src-sh">sudo docker run gregoryschwartz/birch-beer:0.1.0.0 -h
</pre>
</div>
<p>
To build the <code>birch-beer</code> image yourself if you want:
</p>
<div class="org-src-container">
<pre class="src src-sh">git clone https://github.com/GregorySchwartz/birch-beer.git
<span style="color: #ff8700;">cd</span> birch-beer
docker build -t birch-beer -f ./Dockerfile .
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="outline-container-org7da20b4" class="outline-2">
<h2 id="org7da20b4">Usage</h2>
<div class="outline-text-2" id="text-org7da20b4">
<p>
<b>For a more detailed look at many of the features</b>, check out the
<code>too-many-cells</code> <a href="https://github.com/GregorySchwartz/too-many-cells">README</a> about <code>make-tree</code>, which uses <code>birch-beer</code> to plot
single cell clades with examples. At any point, use <code>birch-beer -h</code> to see the
help. The general usage would be:
</p>
<div class="org-src-container">
<pre class="src src-bash">birch-beer --input tree.json --labels-file labels.csv
</pre>
</div>
</div>
<div id="outline-container-org20af828" class="outline-3">
<h3 id="org20af828">Tree format</h3>
<div class="outline-text-3" id="text-org20af828">
<p>
The input tree format should be a <code>json</code> file with a recursive structure. An
object is represented by <code>[{"_distance": DOUBLE, "_item": [STRING]},
[SUBFOREST]]</code>, where <code>"_distance"</code> and <code>"_item"</code> are optional (otherwise use
<code>{}</code>), having <code>"_distance"</code> for inner nodes and <code>"_item"</code> for leaves. Supports
rose trees as well! For example:
</p>
<pre class="example" id="orga79e267">
[{"_distance": 0.8}, [[{"_item": ["1", "2"]}, [[{"_item": ["3", "4", "5"]}, []], [{"_item": ["6", "7"]}, []]]], [{"_item": ["8", "9", "10", "11"]}, []]]]
</pre>
</div>
<div id="outline-container-org471f2dc" class="outline-4">
<h4 id="org471f2dc">Example conversion from R</h4>
<div class="outline-text-4" id="text-org471f2dc">
<p>
To get to the required format, here is an example to get from an R <code>hclust</code> tree
to the appropriate <code>json</code>.
</p>
<div class="org-src-container">
<pre class="src src-R"><span style="color: #d787af;">library</span><span style="color: #008787;">(</span>dendextend<span style="color: #008787;">)</span>
<span style="color: #d787af;">library</span><span style="color: #008787;">(</span>data.tree<span style="color: #008787;">)</span>
<span style="color: #d787af;">library</span><span style="color: #008787;">(</span>jsonlite<span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Get hclust tree.</span>
hc = hclust<span style="color: #008787;">(</span>dist<span style="color: #d75f87;">(</span>USArrests<span style="color: #d75f87;">)</span>, <span style="color: #afaf00;">"ave"</span><span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Get dendrogram.</span>
dend = as.dendrogram<span style="color: #008787;">(</span>hc<span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Get nicely formatted tree from dendrogram.</span>
tree = as.Node<span style="color: #008787;">(</span>dend<span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Convert to JSON</span>
json = toJSON<span style="color: #008787;">(</span>as.list<span style="color: #d75f87;">(</span>tree, mode = <span style="color: #afaf00;">"explicit"</span>, unname = <span style="color: #d787af;">TRUE</span><span style="color: #d75f87;">)</span><span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Write to file</span>
cat<span style="color: #008787;">(</span>json, file = <span style="color: #afaf00;">"tree.json"</span><span style="color: #008787;">)</span>
</pre>
</div>
<p>
Saving this file as <code>tree.json</code>, we continue to format as such (this could be a
single command, but was split to make clearer). Here, we use
<a href="https://stedolan.github.io/jq/"> <code>jq</code> </a>, the command line <code>json</code> processor.
</p>
<div class="org-src-container">
<pre class="src src-bash">cat tree.json <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf") | not) then del(.name) else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then del(.members) | del(.midpoint) | del(.value) | del(.plotHeight) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf")) then ._item = .name | del(.name) else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf") | not) then [{}, [.children[]]] else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf")) then [{_item}, []] else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
> formatted_tree.json
</pre>
</div>
<p>
Then we can see the tree using birch-beer.
</p>
<div class="org-src-container">
<pre class="src src-bash">birch-beer -i formatted_tree.json
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-orgf00c8d8" class="outline-3">
<h3 id="orgf00c8d8">Labels format</h3>
<div class="outline-text-3" id="text-orgf00c8d8">
<p>
To assign labels (and thus colors) to the elements within the tree, make a <code>csv</code>
file with an <code>item,label</code> format. Both columns are treated as strings, so
anything can be used as long as the <code>item</code> column matches the item strings in
the tree. For example to go with the above tree:
</p>
<pre class="example" id="org7f7bf40">
item,label
1,1
2,1
3,2
4,2
5,2
6,3
7,1
8,1
9,3
10,3
11,2
</pre>
</div>
</div>
</div>
<div id="outline-container-org56730ad" class="outline-2">
<h2 id="org56730ad">Select examples</h2>
<div class="outline-text-2" id="text-org56730ad">
</div>
<div id="outline-container-org138221b" class="outline-3">
<h3 id="org138221b">Large tree</h3>
<div class="outline-text-3" id="text-org138221b">
<div id="orgc1bb30b" class="figure">
<p><img src="img/complete_default_tree.png" alt="complete_default_tree.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org4c2efa2" class="outline-3">
<h3 id="org4c2efa2">Number overlay</h3>
<div class="outline-text-3" id="text-org4c2efa2">
<div id="orgeb17f84" class="figure">
<p><img src="img/numbered_pruned_tree.png" alt="numbered_pruned_tree.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org7b1494c" class="outline-3">
<h3 id="org7b1494c">Distance overlay</h3>
<div class="outline-text-3" id="text-org7b1494c">
<div id="org1f83293" class="figure">
<p><img src="img/modularity_pruned_tree.png" alt="modularity_pruned_tree.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org0d7221d" class="outline-3">
<h3 id="org0d7221d">Continuous color saturation</h3>
<div class="outline-text-3" id="text-org0d7221d">
<div id="orgff8e284" class="figure">
<p><img src="img/cd4_saturated_10_dendrogram.png" alt="cd4_saturated_10_dendrogram.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-orgb7a229c" class="outline-3">
<h3 id="orgb7a229c">Continuous multi-color saturation</h3>
<div class="outline-text-3" id="text-orgb7a229c">
<div id="org9e1f052" class="figure">
<p><img src="img/cd4_cd8_sat_10_dendrogram.png" alt="cd4_cd8_sat_10_dendrogram.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org51ecb12" class="outline-3">
<h3 id="org51ecb12">Diversity of labels</h3>
<div class="outline-text-3" id="text-org51ecb12">
<div id="org01f5ba3" class="figure">
<p><img src="img/diversity_pruned_tree.png" alt="diversity_pruned_tree.png" />
</p>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Gregory W. Schwartz</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>