[Patchwork-commits] r118 - in www: . css css/fonts css/fonts/base css/fonts/social css/img css/img/fancybox js
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 16 16:47:36 CEST 2012
Author: sebastian_d
Date: 2012-04-16 16:47:36 +0200 (Mon, 16 Apr 2012)
New Revision: 118
Added:
www/AI_Cov.php
www/DownloadInstall.html
www/README
www/cg_demo.php
www/cg_exec.php
www/cg_inst.php
www/cg_requ.php
www/cg_resu.php
www/css/
www/css/chosen.css
www/css/fonts/
www/css/fonts/base/
www/css/fonts/base/icomoon-webfont.eot
www/css/fonts/base/icomoon-webfont.svg
www/css/fonts/base/icomoon-webfont.ttf
www/css/fonts/base/icomoon-webfont.woff
www/css/fonts/social/
www/css/fonts/social/icomoonsocial-webfont.eot
www/css/fonts/social/icomoonsocial-webfont.svg
www/css/fonts/social/icomoonsocial-webfont.ttf
www/css/fonts/social/icomoonsocial-webfont.woff
www/css/img/
www/css/img/70_HCC1187__KaCh_chr1.png
www/css/img/70_HCC1187_check.png
www/css/img/70_HCC1187_copynumbers_KaChCN_chr1.png
www/css/img/Allelic_plot.png
www/css/img/Demo__KaCh_chr1.png
www/css/img/Fig1pw_tut.png
www/css/img/breadcrumbs-bg.gif
www/css/img/bright_squares.png
www/css/img/chosen-sprite.png
www/css/img/copynumbers_KaChCN_chr1.png
www/css/img/copynumbers_Ka_check.png
www/css/img/copynumbers__karyotypeCN.chr18.png
www/css/img/copynumbers__karyotype_check.png
www/css/img/fancybox/
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www/css/img/fancybox/fancybox.png
www/css/img/fancybox/jquery.easing-1.3.pack.js
www/css/img/fancybox/jquery.fancybox-1.3.4.js
www/css/img/fancybox/jquery.fancybox-1.3.4.pack.js
www/css/img/fancybox/jquery.mousewheel-3.0.4.pack.js
www/css/img/file_struc1.png
www/css/img/file_struct1.png
www/css/img/flowPWreq.png
www/css/img/flowchartCG.png
www/css/img/flowchartPWexec.png
www/css/img/green_chromosome.png
www/css/img/grid.png
www/css/img/icon-arrow-right.png
www/css/img/icon-check.png
www/css/img/purple_chromosome.png
www/css/img/tumor.bam_karyotype.chr18.png
www/css/jquery.fancybox-1.3.4.css
www/css/kickstart-buttons.css
www/css/kickstart-forms.css
www/css/kickstart-grid.css
www/css/kickstart-icons.css
www/css/kickstart-menus.css
www/css/kickstart.css
www/css/prettify.css
www/css/tiptip.css
www/elements.html
www/humans.txt
www/index.php
www/intro.php
www/js/
www/js/dynamicpage.js
www/js/dynload.js
www/js/jquery.ba-hashchange.min.js
www/js/kickstart.js
www/js/popup.js
www/js/prettify.js
www/js/sidebar.js
www/license.txt
www/menu.php
www/pw_demo.php
www/pw_exec.php
www/pw_inst.php
www/pw_requ.php
www/pw_resu.php
www/robots.txt
www/style.css
Log:
Adding homepage content
Added: www/AI_Cov.php
===================================================================
--- www/AI_Cov.php (rev 0)
+++ www/AI_Cov.php 2012-04-16 14:47:36 UTC (rev 118)
@@ -0,0 +1,229 @@
+<html><head>
+
+<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.6.4/jquery.min.js"></script>
+<script type="text/javascript" src="js/prettify.js"></script>
+ <!-- PRETTIFY -->
+<script type="text/javascript" src="js/kickstart.js"></script>
+<link rel="stylesheet" type="text/css" href="css/kickstart.css" media="all" />
+<link rel="stylesheet" type="text/css" href="style.css" media="all" />
+
+</head>
+<body>
+
+<div id="wrap" class="clearfix">
+ <div class="col_12">
+
+ <h4>Allelic Imbalance</h4>
+
+ Allele-specific information is obtained from read counts at heterozygous SNPs.
+
+ <!--
+ Allelic imbalance of a segment is then calculated as
+
+
+ <table class="fraction" cellpadding="0" cellspacing="0">
+ <tr>
+ <td style="text-align:center;" nowrap="nowrap"><i>Σ(Highest allele counts)
+ −Σ(Lowest allele counts)</i>
+ </td>
+ </tr>
+ <tr>
+ <td style="text-align:center;" class="upper_line"><i>Σ(Highest allele counts)</i>
+ </td>
+ </tr>
+ </table>
+
+
+ What this basically does is separate chromosomal regions by their allele constitution. -->
+ Allelic-imbalance basically separates chromosomal regions by their allele constitution.
+ A normal diploid person will have one maternal and one paternal copy of a chromosome.
+ For each copy number there can be losses of segments to either of the
+ chromosomes as well as copies/gains. It is this allele-specific information that our
+ allelic imbalance captures. It does not, however, distinguish the origin of a segment,
+ that is to say that two paternal copies have the same allelic imbalance ratio as two
+ maternal copies. Below is an attempt to explain the different possible allelic combinations
+ for a few copy numbers,
+ it is VERY important that you understand that it is the ratio between green and purple that
+ is important, not if purple/green is maternal/paternal. <br />
+ From an allelic imbalance score point of view
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;"> is the same as
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">. <br /><br />
+
+ <table border="1">
+
+ <tr style="height:66px">
+ <th style="border-bottom:1px solid black;">Copy Number</th>
+ <th colspan=3 style="border-bottom:1px solid black;">Possible segment combinations</th>
+ </tr>
+
+ <tr>
+ <td>1</td>
+ <td><img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;"></td>
+ </tr>
+
+ <tr>
+ <td>2</td>
+ <td><img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ <td><img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ </tr>
+
+ <tr>
+ <td>3</td>
+ <td>
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ <td><img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ </tr>
+
+ <tr>
+ <td>4</td>
+ <td><img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ <td><img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ <td>
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ </tr>
+
+ <tr>
+ <td>5</td>
+ <td><img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ <td>
+ <img src="css/img/purple_chromosome.png" alt="purple segment"
+ title="Purple segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ <td>
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;">
+ <img src="css/img/green_chromosome.png" alt="green segment"
+ title="Green segment" style="display:inline-block;"></td>
+ </tr>
+
+ </table><br />
+
+ Here is a an example of a plot generated using patchworks where I have added the possible
+ allele combinations next to the clusters. <br />
+
+ <img src="css/img/Allelic_plot.png" alt="Allele-specific tutorial" title="Allele-specific graphic guide"
+ style="width:880px;">
+
+ <br /><h4>Coverage</h4>
+
+ Coverage is measured as total DNA content and normalized around 1. You will get a
+ clearer picture at higher coverage data, 120x etc, however patchworkCG has high quality results
+ with low coverage also.
+
+ </div>
+ <div class="clear"></div>
+</div>
+
+<div id="footer">
+ <div id="left">
+ Sebastian DiLorenzo - sebastian.dilorenzo(at)medsci.uu.se <br />
+
+ Markus Mayrhofer - markus.mayrhofer(at)medsci.uu.se <br />
+
+ <br />
+ <br />
+ Last modified: 2012-03-13
+
+ </div>
+ <div style="text-align:right;" id="right">
+ <a href="http://r-forge.r-project.org/" target="_blank" style="text-decoration:none;">
+ R-forge</a> <br />
+ <a href="http://www.completegenomics.com" target="_blank" style="text-decoration:none;">
+ CompleteGenomics</a> <br />
+ <a href="http://www.scilifelab.se/index.php?content=home" target="_blank" style="text-decoration:none;">
+ SciLifeLab</a><br />
+ <a href="http://www.akademiska.se/" target="_blank" style="text-decoration:none;">
+ Akademiska Sjukhuset</a> <br />
+ <a href="http://www.medsci.uu.se" target="_blank" style="text-decoration:none;">
+ Uppsala University Medical Sciences</a> <br />
+ </div>
+ <div class="clear"></div>
+</div>
+
+</body>
+</html>
+
+
+
+
+
+
+
+
+
+
+
Property changes on: www/AI_Cov.php
___________________________________________________________________
Added: svn:executable
+ *
Added: www/DownloadInstall.html
===================================================================
--- www/DownloadInstall.html (rev 0)
+++ www/DownloadInstall.html 2012-04-16 14:47:36 UTC (rev 118)
@@ -0,0 +1,3 @@
+
+Download Locations and ways <br />
+Installation <br />
Property changes on: www/DownloadInstall.html
___________________________________________________________________
Added: svn:executable
+ *
Added: www/README
===================================================================
--- www/README (rev 0)
+++ www/README 2012-04-16 14:47:36 UTC (rev 118)
@@ -0,0 +1,42 @@
+-------------------------------------------------
+HMTL KickStart
+by Joshua Gatcke
+http://www.99lime.com
+Version: 0.92
+-------------------------------------------------
+
+-------------------------------------------------
+What is HTML KickStart?
+-------------------------------------------------
+HTML KickStart is an ultra–lean set of HTML5, CSS, and jQuery (javascript) files, layouts, and elements designed to give you a headstart and save you 10's of hours on your next web project.
+
+HTML KickStart includes everything you need to rapidly create website layouts – things like slideshows, menus, flexible grids, image placeholders, buttons, and more – saving you a ton of time so you can produce faster and make more money.
+
+Bonus! All HTML KickStart Elements are fully Browser tested, they even gracefully degrade ;)
+
+-------------------------------------------------
+Perfect for Wireframing in HTML
+-------------------------------------------------
+HTML KickStart has everything you need to rapidly create HTML Page Layouts, perfect for Wireframing in HTML.
+Layouts that used to take hours now take minutes.
+
+-------------------------------------------------
+Getting Started
+-------------------------------------------------
+1. Download HTML KickStart
+2. Open blank.html in your favorite text editor
+3. Start adding KickStart Elements to blank.html: (http://www.99lime.com/elements/)
+4. Save blank.html and open in your favorite Web Browser
+5. Have fun!
+
+-------------------------------------------------
+HTML KickStart is FREE and Open Source.
+Release Under the MIT Open Source License.
+-------------------------------------------------
+Copyright © 2011-2012 Joshua Gatcke http://www.99lime.com | HTML KickStart
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
\ No newline at end of file
Property changes on: www/README
___________________________________________________________________
Added: svn:executable
+ *
Added: www/cg_demo.php
===================================================================
--- www/cg_demo.php (rev 0)
+++ www/cg_demo.php 2012-04-16 14:47:36 UTC (rev 118)
@@ -0,0 +1,187 @@
+To help you verify that you have installed patchworkCG correctly and that
+it is working we will here use the
+<a href="ftp://ftp2.completegenomics.com/Cancer_pairs/ASM_Build37_2.0.0/HCC2218/GS00258-DNA_B03/" style="text-decoration:none;"
+ target="_blank">publically available cancer data set HCC2218 of CompleteGenomics</a>.
+ <br /><br />
+
+We will go through the exact commands applicable in a typical run of this data and
+ some plots that you can compare your own results with. <br /><br />
+
+ Once you have downloaded the data and unpacked it you should have a file structure
+ resembling the screenshot below. The most important files, which are used in
+ patchworkCG, have been highlighted. <br />
+ <img src="css/img/file_struct1.png" alt="CompleteGenomics ASM"
+title="ASM File structure"> <br /><br />
+
+Now we are ready to start R and issue all the necessary commands, as seen in the
+install and execution tabs.
+
+<pre style="height:500px;overflow:scroll;">
+#For a working directory I chose just above the ASM folder.
+
+➜ GS00258-DNA_B03 ls
+ASM idMap-HCC2218-H-200-37-ASM-T1.tsv
+HCC2218-H-200-37-ASM version
+LIB
+
+#Starting R
+
+➜ GS00258-DNA_B03 R
+
+R version 2.14.1 (2011-12-22)
+Copyright (C) 2011 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+#Install package
+
+> install.packages("patchworkCG", repos="http://R-Forge.R-project.org",type="source")
+trying URL 'http://R-Forge.R-project.org/src/contrib/patchworkCG_1.0.tar.gz'
+Content type 'application/x-gzip' length 669849 bytes (654 Kb)
+opened URL
+==================================================
+downloaded 654 Kb
+
+* installing *source* package 'patchworkCG' ...
+** R
+** data
+** preparing package for lazy loading
+** help
+*** installing help indices
+** building package indices ...
+** testing if installed package can be loaded
+
+* DONE (patchworkCG)
+
+The downloaded packages are in
+ '/private/var/folders/zm/8v842d8n4172k1yc0589p8sw0000gn/T/RtmprYh5Mq/downloaded_packages'
+
+#Load Library
+
+> library(patchworkCG)
+
+#Execute patchwork.CG.plot
+
+> patchwork.CG.plot(path="ASM/",name="Demo_")
+Reading files from ASM folder
+File input complete
+Performing calculations
+Calculations complete
+Saving objects to CG.Rdata
+Initiating Plotting
+Plotting Complete
+patchwork.CG.plot Complete
+ Please read documentation on running patchwork.CG.copynumbers
+
+#Execute patchwork.CG.copynumbers (See execution section for aquiring arguments)
+#Side note: this is a tricky sample as there is no copy number 2 with loss
+#of heterozygosity, but as copynumber 1 has allelic imbalance around 1 and copy number 3
+#also has high allelic imbalance we can estimate that had it existed copy number 2
+#would have had very high allelic imbalance. So we approximate it to 0.96.
+
+> patchwork.CG.copynumbers(cn2=0.9,delta=0.5,het=0.25,hom=0.96)
+Warning message:
+NAs introduced by coercion
+
+#Quit
+
+> q()
+Save workspace image? [y/n/c]: n
+➜ GS00258-DNA_B03 ls
+ASM Demo__KaCh_chr1.png
+CG.Rdata Demo__KaCh_chr10.png
+copynumbers.Rdata Demo__KaCh_chr11.png
+copynumbers_KaChCN_chr1.png Demo__KaCh_chr12.png
+copynumbers_KaChCN_chr10.png Demo__KaCh_chr13.png
+copynumbers_KaChCN_chr11.png Demo__KaCh_chr14.png
+copynumbers_KaChCN_chr12.png Demo__KaCh_chr15.png
+copynumbers_KaChCN_chr13.png Demo__KaCh_chr16.png
+copynumbers_KaChCN_chr14.png Demo__KaCh_chr17.png
+copynumbers_KaChCN_chr15.png Demo__KaCh_chr18.png
+copynumbers_KaChCN_chr16.png Demo__KaCh_chr19.png
+copynumbers_KaChCN_chr17.png Demo__KaCh_chr2.png
+copynumbers_KaChCN_chr18.png Demo__KaCh_chr20.png
+copynumbers_KaChCN_chr19.png Demo__KaCh_chr21.png
+copynumbers_KaChCN_chr2.png Demo__KaCh_chr22.png
+copynumbers_KaChCN_chr20.png Demo__KaCh_chr3.png
+copynumbers_KaChCN_chr21.png Demo__KaCh_chr4.png
+copynumbers_KaChCN_chr22.png Demo__KaCh_chr5.png
+copynumbers_KaChCN_chr3.png Demo__KaCh_chr6.png
+copynumbers_KaChCN_chr4.png Demo__KaCh_chr7.png
+copynumbers_KaChCN_chr5.png Demo__KaCh_chr8.png
+copynumbers_KaChCN_chr6.png Demo__KaCh_chr9.png
+copynumbers_KaChCN_chr7.png Demo__KaCh_chrX.png
+copynumbers_KaChCN_chr8.png Demo__KaCh_chrY.png
+copynumbers_KaChCN_chr9.png Demo__karyotype.png
+copynumbers_KaChCN_chrX.png HCC2218-H-200-37-ASM
+copynumbers_KaChCN_chrY.png LIB
+copynumbers_Ka_check.png idMap-HCC2218-H-200-37-ASM-T1.tsv
+Copynumbers.csv version
+</pre>
+
+If successfull your working directory should now contain:
+<ul class="checks">
+ <li>50 plots</li>
+ <li>CG.Rdata</li>
+ <li>copynumbers.Rdata</li>
+ <li>Copynumbers.csv</li>
+</ul>
+<br />
+Here are three of the plots generated during the demo run to validate your plots with. <br /><br />
+
+
+<a href="css/img/Demo__KaCh_chr1.png" target="_blank" style="text-decoration:none;">
+ Demo__KaCh_chr1.png</a><br />
+<!-- <img src="css/img/Demo__KaCh_chr1.png" alt="Output patchwork.CG.plot"
+title="Chromosome 1, patchwork.CG.plot" width=880px> -->
+
+
+<a href="css/img/copynumbers_KaChCN_chr1.png" target="_blank" style="text-decoration:none;">
+ copynumbers_KaChCN_chr1.png</a><br />
+
+<!-- <img src="css/img/copynumbers_KaChCN_chr1.png" alt="Output1 patchwork.CG.copynumbers"
+title="Chromsome 1, patchwork.CG.copynumbers" width=880px> -->
+
+<a href="css/img/copynumbers_Ka_check.png" target="_blank" style="text-decoration:none;">
+ copynumbers_Ka_check.png</a><br />
+
+<!-- <img src="css/img/copynumbers_Ka_check.png" alt="Output2 patchwork.CG.copynumbers"
+title="Whole Genome, Check" width=880px><br /><br /> -->
+
+<br /> <br /> Please feel free to contact us with any queries!
+
+<br /><br /><div style="text-align:center;"><a href="#top" style="text-decoration:none;">Top</a></div>
+
+
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+
Property changes on: www/cg_demo.php
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Added: svn:executable
+ *
Added: www/cg_exec.php
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+<!-- Flowchart -->
+<div style="text-align:center;">
+<img id="flowchartcg" src="css/img/flowchartCG.png"
+alt="Flowchart of processes and data for patchworkCG" title="Flowchart of data and processes for patchworkCG">
+</div><br />
+
+<h4>patchwork.CG.plot()</h4>
+
+patchwork.CG.plot() is a function that visualizes allele-specific copy numbers from the
+whole-genome sequenced data of tumors. <br /><br />
+It is recommended that you run patchworkCG from a "clean" working directory.
+In this way you do not run the risk of having files write over eachother when
+ you run multiple different samples.<br /><br />
+
+In the R environment load the patchworkCG library: <br />
+
+<pre>
+ library(patchworkCG)
+</pre>
+
+Read the excellent documentation for patchwork.CG.plot(): <br />
+
+<pre>
+ ?patchwork.CG.plot
+</pre>
+
+Excerpt from ?patchwork.CG.plot regarding usage and arguments: <br />
+
+<pre>
+ Usage:
+
+ patchwork.CG.plot(path,name='CG_sample',manual_file_input=FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL,
+ depthOfCoverage=NULL)
+
+ Arguments:
+
+ path: Path to the ASM folder. One of the subfolders of your
+ completegenomics directory.
+ name: Default is 'CG_sample'. The name you wish associated with
+ the plots that will be generated.
+ manual_file_input: Default is FALSE. If you set it to TRUE you will be
+ prompted to provide path and filename for the masterVarBeta,
+ somaticCnvSegmentsNondiploid and depthOfCoverage file.
+ masterVarBeta: Path to and COMPLETE NAME of the masterVarBeta file,
+ should you wish to implement it directly. Useful if you want
+ to run the program on multiple samples and wish to create a
+ script going from file to file. This saves you from having to
+ conserve the CompleteGenomics file structure. Default is
+ NULL.
+ somaticCnvSegments: Path to and COMPLETE NAME of the somaticCnvSegments
+ file, should you wish to implement it directly. Useful if you
+ want to run the program on multiple samples and wish to
+ create a script going from file to file. This saves you from
+ having to conserve the CompleteGenomics file structure.
+ Default is NULL.
+ depthOfCoverage: Path to and COMPLETE NAME of the depthOfCoverage file,
+ should you wish to implement it directly. Useful if you want
+ to run the program on multiple samples and wish to create a
+ script going from file to file. This saves you from having to
+ conserve the CompleteGenomics file structure. Default is
+ NULL.
+</pre>
+
+Example run of patchwork.CG.plot() where output has been left for display: <br />
+
+<pre>
+ patchwork.CG.plot(path="path/to/ASM/")
+
+ Reading files from ASM folder
+ File input complete
+ Performing calculations
+ Calculations complete
+ Saving objects to CG.Rdata
+ Initiating Plotting
+ Plotting Complete
+ patchwork.CG.plot Complete
+ Please read documentation on running patchwork.CG.copynumbers
+</pre>
+
+Once it is complete there should be several plots in your working directory as
+well as the file "CG.Rdata". <br /><br />
+
+Execution should take no longer than half an hour, depending on your system.<br /><br />
+
+<h4>patchwork.CG.copynumbers()</h4>
+
+patchwork.CG.copynumbers() is a function that determines which relationship between coverage
+ and allelic imbalance signifies which copy number and allele ratio for each segment.<br /><br />
+
+Running patchwork.CG.copynumbers() requires the aforementioned CG.Rdata file, the function
+will find it automatically if it is in your working directory. There is also
+the option to point to the file using the "CGfile" argument of the function.<br /><br />
+
+Read the documentation for patchwork.CG.copynumbers(): <br />
+
+<pre>
+ ?patchwork.CG.copynumbers
+</pre>
+
+Excerpt from ?patchwork.CG.copynumbers regarding usage and arguments: <br />
+
+<pre>
+ Usage:
+
+ patchwork.CG.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",
+ CGfile=NULL,forcedelta=F)
+
+Arguments:
+
+ cn2: The approximate position of copy number 2, diploid, on total
+ intensity axis.
+ delta: The difference in total intensity between consecutive copy
+ numbers. For example 1 and 2 or 2 and 3. If copy number 2
+ has total intensity ~0.6 and copy number 3 har total
+ intensity ~0.8 then delta would be 0.2.
+ het: Allelic imbalance ratio of heterozygous copy number 2.
+ hom: Allelic imbalance ratio of Loss-of-Heterozygosity copy number
+ 2.
+ maxCn: Highest copy number to calculate for. Default is 8.
+ ceiling: Default is 1.
+ name: Default is "copynumbers_". The name you want attached to generated
+ plots.
+ CGfile: Default is NULL. If your CG.Rdata file is not in your working
+ directory, and you dont wish to move it to your working
+ directory, you can simply input the path here as CGfile =
+ "path/to/file/CG.Rdata" so patchwork.CG.copynumbers() can find its
+ data.
+forcedelta: Default is FALSE. If TRUE the delta value will be absolute
+ and not subject to adjustments.
+</pre>
+
+To infer the arguments for patchwork.CG.copynumbers() you will need to look at one of the chromosomal
+ plots generated using patchwork.CG.plot(). Here is the topmost section of one such plot with some added bars
+ and text for tutorial purposes. The plot shows the whole genome in grey and the chosen chromosome, not
+ important in this guide, in red to blue gradient. From this whole genome picture you can then use the
+ arrangement of the clustered areas to estimate copy numbers and allele-specific information. <br /><br />
+
+<img id="fig1cg" src="css/img/Fig1pw_tut.png"
+alt="Input arguments patchwork.CG.copynumbers" title="Figure 1 patchworkCG"
+ style="width:880px"><br /><br />
+
+The <b>cn2</b> argument is the position of copy number 2. In this example cn2 is ~0.8.<br />
+The <b>delta</b> argument is the difference between two copynumbers on the coverage axis. In this example we
+used copy number 2 and copy number 3, but we could as well have used copy number 2 and the unmarked copy number
+1 to the left of copy number 2. Delta does not take negative argument input. In this example delta is ~0.28.<br />
+The <b>het</b> argument is the position of heterzygous copy number 2 on the allelic imbalance axis. In this example
+het is ~0.21.<br />
+The <b>hom</b> argument is the position of homozygous, loss-of-heterozygosity, copy number 2 on the allelic imbalance
+axis. In this example hom is ~0.79. <br /><br />
+
+Usually you do not need to bother with <b>maxCn</b> and <b>ceiling</b> arguments. <br /><br />
+
+There is more information on interpreting the plots in the results tab which
+may aid you in determining the parameters. <br /><br />
+
+An example run of patchwork.CG.copynumbers(): <br />
+
+<pre>
+ patchwork.CG.copynumbers(cn2=0.8, delta=0.28, het=0.21, hom=0.79, CGfile="path/to/CG.Rdata")
+</pre>
+
+This will generate an additional set of plots in your working directory. <br /><br />
+
+
+<br /><br /><div style="text-align:center;"><a href="#top" style="text-decoration:none;">Top</a></div>
+
+
+
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Property changes on: www/cg_exec.php
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Added: svn:executable
+ *
Added: www/cg_inst.php
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+Begin by starting R. It is recommended that you use the latest version.
+
+<br /><br />
+Issue the following commands within R to install patchworkCG.
+
+<pre>
+ install.packages("patchworkCG", repos="http://R-Forge.R-project.org")
+</pre>
+
+If for some reason that does not work add the 'type="source"' to it, as so:
+
+<pre>
+ install.packages("patchworkCG", repos="http://R-Forge.R-project.org",type="source")
+</pre>
+
+If something still does not work with installation, here is a link to the location of the source files: <br />
+
+<a href="http://r-forge.r-project.org/R/?group_id=1250" target="_blank" style="text-decoration:none">
+ Patchwork</a>
Property changes on: www/cg_inst.php
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Added: svn:executable
+ *
Added: www/cg_requ.php
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--- www/cg_requ.php (rev 0)
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+
+To succesfully run patchworkCG you will need an unpacked
+
+<a href="http://media.completegenomics.com/documents/DataFileFormats+Cancer+Pipeline+2.0.pdf"
+target="_blank" style="text-decoration:none;">
+CompleteGenomics tumor genome data ASM directory</a>.<br />
+Specifically the files ASM/masterVarBeta, CNV/depthOfCoverage and CNV/somaticCnvSegmentsNondiploidBeta are used. <br /><br />
+
+Here are some helpful commands for unpacking your CompleteGenomics data (UNIX).<br /><br />
+To unpack .tar files:<br />
+<pre>
+ tar -zxvf filename.tar
+</pre>
+
+To unpack .bz2 files: <br />
+<pre>
+ bunzip2 filename.bz2
+</pre>
\ No newline at end of file
Property changes on: www/cg_requ.php
___________________________________________________________________
Added: svn:executable
+ *
Added: www/cg_resu.php
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+<h4>Plots of patchwork.CG.plot()</h4>
+
+Here is an example plot of chromosome 1, 70% tumor cells, generated from HCC1187.<br />
+After running patchwork.CG.plot() you should have 24 of these in your working directory, one for
+each chromosome.<br /><br />
+
+For information regarding allelic imbalance and coverage click <a href="AI_Cov.php" target="_blank" style="text-decoration:none;">here</a>.
+
+<h5>Top part of the plot</h5>
+
+The clusters in the plot display regions of certain allelic constitution and copy number.
+The copy number increases along the Coverage axis while paternal/maternal allele ratio
+becomes less balanced along the Allelic Imbalance axis.<br /><br />
+
+The chromosome in question is colored against a background of the complete genome in grey.
+A colored circles gradient and size correlate with its segments position and size on the
+ chromosome. Colors of segments match in regard to all three parts of the plot.
+ The circles are semi-transparent so a darker hue, both for colored and grey,
+ indicate greater amount of genomic content in that region.<br /><br />
+
+We know that each cluster has a certain copy number and allele content and we know that
+a human is usually diploid (copy number 2, heterozygous). Finally we know that the average
+copy number of the genome in question is at position 1 on the Coverage axis.
+We can use this information to determine the clusters probable copy number
+and allele content.<br /><br />
+
+The far left cluster is the deletions, copy number 1. After copy number 1 we
+see two clusters, albeit the lower one does not have much content. This is pretty
+close to Coverage of 1 and as such they are most likely the two allelic states of copy number 2.
+Continuing with this reasoning the next set of clusters is copy number 3, etc.
+
+This arrangement of the genome is easier to see from one of the plots generated by
+patchwork.CG.copynumbers(), or in our section above on allelic imbalance, however before using
+ that function you will need to be able to determine the constitution of the tumor
+ genome as it is used as input arguments for patchwork.CG.copynumbers()!
+
+<img id="fig2cg" src="css/img/70_HCC1187__KaCh_chr1.png" alt="Results example patchwork.CG.plot"
+ title="Figure 2 patchworkCG"
+ style="width:880px"><br /><br />
+
+<h5>Middle part of the plot</h5>
+
+The chromosome in questions coverage plotted against the position on the chromosome.
+Note how the segments colors match the Top circles and Bottom segments.
+
+<h5>Bottom part of the plot</h5>
+
+The chromosome in questions allelic imbalance plotted against the
+position on the chromosome.
+
+<br /><br /><h4>Plots of patchwork.CG.copynumbers()</h4>
+
+This plot, arbitrarily named "check", is not chromosome specific and shows
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/patchwork -r 118
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