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432 <tr>
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433 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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434 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Setup R error handling to go to stderr</span></td>
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435 </tr>
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437 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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438 <td id="LC2" class="blob-code blob-code-inner js-file-line">options(<span class="pl-v">show.error.messages</span><span class="pl-k">=</span><span class="pl-c1">F</span>, <span class="pl-v">error</span><span class="pl-k">=</span><span class="pl-k">function</span>(){cat(geterrmessage(),<span class="pl-v">file</span><span class="pl-k">=</span>stderr());q(<span class="pl-s"><span class="pl-pds">"</span>no<span class="pl-pds">"</span></span>,<span class="pl-c1">1</span>,<span class="pl-c1">F</span>)})</td>
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446 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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447 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> We need to not crash galaxy with an UTF8 error on German LC settings.</span></td>
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448 </tr>
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449 <tr>
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450 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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451 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">loc</span> <span class="pl-k"><-</span> Sys.setlocale(<span class="pl-s"><span class="pl-pds">"</span>LC_MESSAGES<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>en_US.UTF-8<span class="pl-pds">"</span></span>)</td>
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464 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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465 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Import library</span></td>
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468 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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469 <td id="LC9" class="blob-code blob-code-inner js-file-line">library(<span class="pl-s"><span class="pl-pds">"</span>getopt<span class="pl-pds">"</span></span>)</td>
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470 </tr>
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473 <td id="LC10" class="blob-code blob-code-inner js-file-line">library(<span class="pl-s"><span class="pl-pds">"</span>RColorBrewer<span class="pl-pds">"</span></span>)</td>
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474 </tr>
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477 <td id="LC11" class="blob-code blob-code-inner js-file-line">library(<span class="pl-s"><span class="pl-pds">"</span>gplots<span class="pl-pds">"</span></span>)</td>
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478 </tr>
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481 <td id="LC12" class="blob-code blob-code-inner js-file-line">options(<span class="pl-v">stringAsfactors</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-v">useFancyQuotes</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>)</td>
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485 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Take in trailing command line arguments</span></td>
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486 </tr>
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487 <tr>
|
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488 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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489 <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">args</span> <span class="pl-k"><-</span> commandArgs(<span class="pl-v">trailingOnly</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</td>
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490 </tr>
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491 <tr>
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492 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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493 <td id="LC15" class="blob-code blob-code-inner js-file-line">
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494 </td>
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495 </tr>
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496 <tr>
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497 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
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498 <td id="LC16" class="blob-code blob-code-inner js-file-line">
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499 </td>
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500 </tr>
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501 <tr>
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502 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
|
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503 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> get options, using the spec as defined by the enclosed list.</span></td>
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504 </tr>
|
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505 <tr>
|
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506 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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|
507 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> we read the options from the default: commandArgs(TRUE).</span></td>
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508 </tr>
|
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509 <tr>
|
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510 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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511 <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-v">option_specification</span> <span class="pl-k">=</span> <span class="pl-k">matrix</span>(c(</td>
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512 </tr>
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513 <tr>
|
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514 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
|
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515 <td id="LC20" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>input<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>i<span class="pl-pds">'</span></span>, <span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td>
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516 </tr>
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|
517 <tr>
|
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518 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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519 <td id="LC21" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>title<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>t<span class="pl-pds">'</span></span>,<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td>
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520 </tr>
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|
521 <tr>
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|
522 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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|
|
523 <td id="LC22" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>transform<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>c<span class="pl-pds">'</span></span>, <span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td>
|
|
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524 </tr>
|
|
|
525 <tr>
|
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|
526 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
|
|
|
527 <td id="LC23" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>keylabel<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>k<span class="pl-pds">'</span></span>,<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span>,</td>
|
|
|
528 </tr>
|
|
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529 <tr>
|
|
|
530 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
|
|
|
531 <td id="LC24" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">'</span>output<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>o<span class="pl-pds">'</span></span>, <span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">'</span>character<span class="pl-pds">'</span></span></td>
|
|
|
532 </tr>
|
|
|
533 <tr>
|
|
|
534 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
|
|
|
535 <td id="LC25" class="blob-code blob-code-inner js-file-line"> ), <span class="pl-v">byrow</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>, <span class="pl-v">ncol</span><span class="pl-k">=</span><span class="pl-c1">4</span>);</td>
|
|
|
536 </tr>
|
|
|
537 <tr>
|
|
|
538 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
|
|
|
539 <td id="LC26" class="blob-code blob-code-inner js-file-line">
|
|
|
540 </td>
|
|
|
541 </tr>
|
|
|
542 <tr>
|
|
|
543 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
|
|
|
544 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Parse options</span></td>
|
|
|
545 </tr>
|
|
|
546 <tr>
|
|
|
547 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
|
|
|
548 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-v">options</span> <span class="pl-k">=</span> getopt(<span class="pl-smi">option_specification</span>);</td>
|
|
|
549 </tr>
|
|
|
550 <tr>
|
|
|
551 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
|
|
|
552 <td id="LC29" class="blob-code blob-code-inner js-file-line">
|
|
|
553 </td>
|
|
|
554 </tr>
|
|
|
555 <tr>
|
|
|
556 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
|
|
|
557 <td id="LC30" class="blob-code blob-code-inner js-file-line">
|
|
|
558 </td>
|
|
|
559 </tr>
|
|
|
560 <tr>
|
|
|
561 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
|
|
|
562 <td id="LC31" class="blob-code blob-code-inner js-file-line">
|
|
|
563 </td>
|
|
|
564 </tr>
|
|
|
565 <tr>
|
|
|
566 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
|
|
|
567 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> Print options to see what is going on</span></td>
|
|
|
568 </tr>
|
|
|
569 <tr>
|
|
|
570 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
|
|
|
571 <td id="LC33" class="blob-code blob-code-inner js-file-line">cat(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span> input: <span class="pl-pds">"</span></span>,<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">input</span>)</td>
|
|
|
572 </tr>
|
|
|
573 <tr>
|
|
|
574 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
|
|
|
575 <td id="LC34" class="blob-code blob-code-inner js-file-line">cat(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span> title: <span class="pl-pds">"</span></span>,<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">title</span>)</td>
|
|
|
576 </tr>
|
|
|
577 <tr>
|
|
|
578 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
|
|
|
579 <td id="LC35" class="blob-code blob-code-inner js-file-line">cat(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span> output: <span class="pl-pds">"</span></span>,<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">output</span>)</td>
|
|
|
580 </tr>
|
|
|
581 <tr>
|
|
|
582 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
|
|
|
583 <td id="LC36" class="blob-code blob-code-inner js-file-line">
|
|
|
584 </td>
|
|
|
585 </tr>
|
|
|
586 <tr>
|
|
|
587 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
|
|
|
588 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">input</span> <span class="pl-k"><-</span> read.delim(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">input</span>,<span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>,<span class="pl-v">header</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>)</td>
|
|
|
589 </tr>
|
|
|
590 <tr>
|
|
|
591 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
|
|
|
592 <td id="LC38" class="blob-code blob-code-inner js-file-line">
|
|
|
593 </td>
|
|
|
594 </tr>
|
|
|
595 <tr>
|
|
|
596 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
|
|
|
597 <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">mat_input</span> <span class="pl-k"><-</span> data.matrix(<span class="pl-smi">input</span>[,<span class="pl-c1">2</span><span class="pl-k">:</span>ncol(<span class="pl-smi">input</span>)]) </td>
|
|
|
598 </tr>
|
|
|
599 <tr>
|
|
|
600 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
|
|
|
601 <td id="LC40" class="blob-code blob-code-inner js-file-line">
|
|
|
602 </td>
|
|
|
603 </tr>
|
|
|
604 <tr>
|
|
|
605 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
|
606 <td id="LC41" class="blob-code blob-code-inner js-file-line">
|
|
|
607 </td>
|
|
|
608 </tr>
|
|
|
609 <tr>
|
|
|
610 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
|
|
|
611 <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>){</td>
|
|
|
612 </tr>
|
|
|
613 <tr>
|
|
|
614 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
|
|
|
615 <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> <span class="pl-smi">mat_input</span></td>
|
|
|
616 </tr>
|
|
|
617 <tr>
|
|
|
618 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
|
|
|
619 <td id="LC44" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log2<span class="pl-pds">"</span></span>){</td>
|
|
|
620 </tr>
|
|
|
621 <tr>
|
|
|
622 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
|
|
|
623 <td id="LC45" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log2(<span class="pl-smi">mat_input</span>)</td>
|
|
|
624 </tr>
|
|
|
625 <tr>
|
|
|
626 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
|
|
|
627 <td id="LC46" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log2plus1<span class="pl-pds">"</span></span>){</td>
|
|
|
628 </tr>
|
|
|
629 <tr>
|
|
|
630 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
|
|
|
631 <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log2(<span class="pl-smi">mat_input</span><span class="pl-k">+</span><span class="pl-c1">1</span>)</td>
|
|
|
632 </tr>
|
|
|
633 <tr>
|
|
|
634 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
|
|
|
635 <td id="LC48" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log10<span class="pl-pds">"</span></span>){</td>
|
|
|
636 </tr>
|
|
|
637 <tr>
|
|
|
638 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
|
|
|
639 <td id="LC49" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log10(<span class="pl-smi">mat_input</span>)</td>
|
|
|
640 </tr>
|
|
|
641 <tr>
|
|
|
642 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
|
|
|
643 <td id="LC50" class="blob-code blob-code-inner js-file-line">}<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">transform</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>log10plus1<span class="pl-pds">"</span></span>){</td>
|
|
|
644 </tr>
|
|
|
645 <tr>
|
|
|
646 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
|
|
|
647 <td id="LC51" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">linput</span> <span class="pl-k"><-</span> log10(<span class="pl-smi">mat_input</span><span class="pl-k">+</span><span class="pl-c1">1</span>)</td>
|
|
|
648 </tr>
|
|
|
649 <tr>
|
|
|
650 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
|
|
|
651 <td id="LC52" class="blob-code blob-code-inner js-file-line"> }<span class="pl-k">else</span>{</td>
|
|
|
652 </tr>
|
|
|
653 <tr>
|
|
|
654 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
|
|
|
655 <td id="LC53" class="blob-code blob-code-inner js-file-line">}</td>
|
|
|
656 </tr>
|
|
|
657 <tr>
|
|
|
658 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
|
|
|
659 <td id="LC54" class="blob-code blob-code-inner js-file-line">
|
|
|
660 </td>
|
|
|
661 </tr>
|
|
|
662 <tr>
|
|
|
663 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
|
|
|
664 <td id="LC55" class="blob-code blob-code-inner js-file-line">
|
|
|
665 </td>
|
|
|
666 </tr>
|
|
|
667 <tr>
|
|
|
668 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
|
|
|
669 <td id="LC56" class="blob-code blob-code-inner js-file-line">
|
|
|
670 </td>
|
|
|
671 </tr>
|
|
|
672 <tr>
|
|
|
673 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
|
|
|
674 <td id="LC57" class="blob-code blob-code-inner js-file-line"><span class="pl-v">hclust_fun</span> <span class="pl-k">=</span> <span class="pl-k">function</span>(<span class="pl-smi">x</span>) hclust(<span class="pl-smi">x</span>, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>complete<span class="pl-pds">"</span></span>)</td>
|
|
|
675 </tr>
|
|
|
676 <tr>
|
|
|
677 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
|
|
|
678 <td id="LC58" class="blob-code blob-code-inner js-file-line"><span class="pl-v">dist_fun</span> <span class="pl-k">=</span> <span class="pl-k">function</span>(<span class="pl-smi">x</span>) dist(<span class="pl-smi">x</span>, <span class="pl-v">method</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>maximum<span class="pl-pds">"</span></span>)</td>
|
|
|
679 </tr>
|
|
|
680 <tr>
|
|
|
681 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
|
|
|
682 <td id="LC59" class="blob-code blob-code-inner js-file-line">
|
|
|
683 </td>
|
|
|
684 </tr>
|
|
|
685 <tr>
|
|
|
686 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
|
|
|
687 <td id="LC60" class="blob-code blob-code-inner js-file-line">pdf(<span class="pl-v">file</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>Rplot.pdf<span class="pl-pds">"</span></span>)</td>
|
|
|
688 </tr>
|
|
|
689 <tr>
|
|
|
690 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
|
|
|
691 <td id="LC61" class="blob-code blob-code-inner js-file-line"><span class="pl-smi">colfunc</span> <span class="pl-k"><-</span> colorRampPalette(c(<span class="pl-s"><span class="pl-pds">"</span>white<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>red<span class="pl-pds">"</span></span>))</td>
|
|
|
692 </tr>
|
|
|
693 <tr>
|
|
|
694 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
|
|
|
695 <td id="LC62" class="blob-code blob-code-inner js-file-line">heatmap.2(<span class="pl-smi">linput</span>,</td>
|
|
|
696 </tr>
|
|
|
697 <tr>
|
|
|
698 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
|
|
|
699 <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">distfun</span><span class="pl-k">=</span><span class="pl-smi">dist_fun</span>, <span class="pl-v">hclustfun</span><span class="pl-k">=</span><span class="pl-smi">hclust_fun</span>, <span class="pl-v">scale</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>,</td>
|
|
|
700 </tr>
|
|
|
701 <tr>
|
|
|
702 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
|
|
|
703 <td id="LC64" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">col</span><span class="pl-k">=</span>colfunc(<span class="pl-c1">50</span>), <span class="pl-v">trace</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>, <span class="pl-v">density.info</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>none<span class="pl-pds">"</span></span>,<span class="pl-v">labRow</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>, <span class="pl-v">margins</span><span class="pl-k">=</span>c(<span class="pl-c1">8</span>,<span class="pl-c1">2</span>),</td>
|
|
|
704 </tr>
|
|
|
705 <tr>
|
|
|
706 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
|
|
|
707 <td id="LC65" class="blob-code blob-code-inner js-file-line"> <span class="pl-v">main</span> <span class="pl-k">=</span> <span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">title</span>, <span class="pl-v">key.xlab</span><span class="pl-k">=</span> <span class="pl-smi">options</span><span class="pl-k">$</span><span class="pl-smi">keylabel</span>, <span class="pl-v">keysize</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td>
|
|
|
708 </tr>
|
|
|
709 <tr>
|
|
|
710 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
|
|
|
711 <td id="LC66" class="blob-code blob-code-inner js-file-line">dev.off()</td>
|
|
|
712 </tr>
|
|
|
713 </table>
|
|
|
714
|
|
|
715 </div>
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716
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|
|
717 </div>
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718
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719 <button type="button" data-facebox="#jump-to-line" data-facebox-class="linejump" data-hotkey="l" class="d-none">Jump to Line</button>
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720 <div id="jump-to-line" style="display:none">
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|
|
721 <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div>
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|
722 <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus>
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723 <button type="submit" class="btn">Go</button>
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724 </form></div>
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725
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726 </div>
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|
727 <div class="modal-backdrop js-touch-events"></div>
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728 </div>
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729
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730
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731
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732
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733 </div>
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734 </div>
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735
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736 </div>
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737
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738 <div class="container site-footer-container">
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739 <div class="site-footer" role="contentinfo">
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740 <ul class="site-footer-links float-right">
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741 <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact GitHub</a></li>
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742 <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
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743 <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
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744 <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li>
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745 <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
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746 <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li>
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747
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748 </ul>
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749
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750 <a href="https://github.com" aria-label="Homepage" class="site-footer-mark" title="GitHub">
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751 <svg aria-hidden="true" class="octicon octicon-mark-github" height="24" version="1.1" viewBox="0 0 16 16" width="24"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
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752 </a>
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753 <ul class="site-footer-links">
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754 <li>© 2017 <span title="0.05906s from github-fe126-cp1-prd.iad.github.net">GitHub</span>, Inc.</li>
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755 <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li>
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756 <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li>
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757 <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li>
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758 <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
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759 <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li>
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760 </ul>
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761 </div>
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762 </div>
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763
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764
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765
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766
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767
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768 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
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769 <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg>
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770 <button type="button" class="flash-close js-flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
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771 <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48z"/></svg>
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772 </button>
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773 You can't perform that action at this time.
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774 </div>
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775
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776
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777 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/compat-8e19569aacd39e737a14c8515582825f3c90d1794c0e5539f9b525b8eb8b5a8e.js"></script>
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778 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-d192e80fd36e12d318d28c466a8998ebca9d20a15a38122f99edfe44612a034b.js"></script>
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779 <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-7cd1a3faa8feb07795d62d9f1252be656d0cdb2aac27d8b7649c2ceb307a7a8c.js"></script>
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780
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781
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782
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783
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784 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner d-none">
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785 <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg>
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786 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
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787 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
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788 </div>
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789 <div class="facebox" id="facebox" style="display:none;">
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790 <div class="facebox-popup">
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791 <div class="facebox-content" role="dialog" aria-labelledby="facebox-header" aria-describedby="facebox-description">
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792 </div>
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793 <button type="button" class="facebox-close js-facebox-close" aria-label="Close modal">
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794 <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48z"/></svg>
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795 </button>
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796 </div>
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797 </div>
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798
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799
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800 </body>
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801 </html>
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802
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