Merge branch 'master' of ssh://github.com/CGATOxford/cgat

CGATPipelines/pipeline_docs/pipeline_rrbs/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinxreport-build --num-jobs=4 sphinx-build
+SPHINXCLEAN   = sphinxreport-clean
+PAPER         =
+
+PUBLISH       = ~/public_html/SphinxReport
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+PORT=8080
+
+.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html      to make standalone HTML files"
+	@echo "  dirhtml   to make HTML files named index.html in directories"
+	@echo "  pickle    to make pickle files"
+	@echo "  json      to make JSON files"
+	@echo "  htmlhelp  to make HTML files and a HTML help project"
+	@echo "  qthelp    to make HTML files and a qthelp project"
+	@echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  changes   to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck to check all external links for integrity"
+	@echo "  doctest   to run all doctests embedded in the documentation (if enabled)"
+	@echo "  publish   to copy the html code to public_html"
+
+clean:
+	$(SPHINXCLEAN) clean
+
+distclean:
+	$(SPHINXCLEAN) distclean
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
+	@echo
+	@echo "Build finished. The HTML pages are in _build/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in _build/dirhtml."
+
+server-start:
+	if ! test -e static; then ln -s _build/html static; fi 
+	nohup nice -19 python ./server.py $(PORT) 2>&1 >> server.log &
+
+server-stop:
+	pkill "server.py $(PORT)"
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) _build/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) _build/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) _build/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in _build/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) _build/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in _build/qthelp, like this:"
+	@echo "# qcollectiongenerator _build/qthelp/Test.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile _build/qthelp/Test.qhc"
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in _build/latex."
+	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+	      "run these through (pdf)latex."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) _build/changes
+	@echo
+	@echo "The overview file is in _build/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) _build/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in _build/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) _build/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in _build/doctest/output.txt."
+
+publish:
+	rm -rf $(PUBLISH)
+	mkdir $(PUBLISH)
+	cp -r _build/html/* $(PUBLISH)/

CGATPipelines/pipeline_docs/pipeline_rrbs/_templates/index.html

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+{% extends "layout.html" %}
+{% set title = 'Analysis pipeline' %}
+
+{% block body %}
+<h1>Exome Pipeline Home</h1>
+<p>
+Welcome to the results of the exome pipeline. 
+This set of pages gives summary statistics for the alignment of NGS reads to a target genome and the subsequent calling of sequence variants. 
+Variants discivered using this pipelien can be functionaly profiled using the variant annotation pipeline.
+</p>
+<p>
+<a HREF="pipeline.html">Pipeline Section</a>.
+<p>
+</p>
+
+{% endblock %}

CGATPipelines/pipeline_docs/pipeline_rrbs/_templates/indexsidebar.html

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+<h3>Download</h3>
+<p>Current version: <b>{{ version }}</b></p>
+
+<p>Download matplotlib from the sourceforge <a
+href="http://sourceforge.net/projects/matplotlib">project</a> page
+(but first take a look at the <a href="{{ pathto('users/installing')
+}}">installing</a> page).  Here's a summary of <a href="{{
+pathto('users/whats_new') }}">what's new</a>. </p>
+
+<p>There are several matplotlib addon <a href="{{
+pathto('users/toolkits') }}">toolkits</a>, including the projection
+and mapping toolkit
+<a href="http://matplotlib.sf.net/basemap/doc/html">basemap</a>.</p>
+
+<p>Please <a href="http://sourceforge.net/project/project_donations.php?group_id=80706">donate</a>
+to support matplotlib development.</p>
+
+<h3>Need help?</h3>
+
+<p>Check the <a href="{{ pathto('users/index') }}">user</a> guide,
+the <a href="{{ pathto('faq/index') }}">faq</a>, the <a href="{{
+pathto('api/index') }}">api</a> docs,
+<a href="http://www.nabble.com/matplotlib---users-f2906.html">archives</a>,
+and join the matplotlib
+mailing <a href="http://sourceforge.net/mail/?group_id=80706">lists</a>.
+The <a href="{{ pathto('search') }}">search</a> tool searches all of
+the documentation, including full text search of almost 300 complete
+examples which exercise almost every corner of matplotlib.</p>
+
+<p>You can file bugs, patches and feature requests on the
+sourceforge
+<a href="http://sourceforge.net/tracker2/?group_id=80706">tracker</a>,
+but it is a good idea to ping us on the mailing list too.</p>
+
+<p>For details on what's new, see the detailed <a href="{{
+pathto('_static/CHANGELOG', 1) }}">changelog</a>.  Anything that could
+require changes to your existing codes is logged in the <a href="{{
+pathto('api/api_changes.html', 1) }}">api changes</a> file.</p>
+
+<h3>Other stuff</h3>
+
+<p>The matplotlib <a href="{{ pathto('users/license') }}">license</a>
+is based on the Python Software Foundation
+<a href="http://www.python.org/psf/license">(PSF)</a> license.</p>
+
+<p>There is an active developer community and a long list of people
+who have made significant <a href="{{ pathto('users/credits')
+}}">contributions</a>.</p>
+

CGATPipelines/pipeline_docs/pipeline_rrbs/_templates/layout.html

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+{% extends "!layout.html" %}
+
+{% block rootrellink %}
+<li><a href="{{ pathto('index') }}">home</a>|&nbsp;</li>
+<li><a href="{{ pathto('search') }}">search</a>|&nbsp;</li>
+<li><a href="{{ pathto('pipeline') }}">pipeline</a>|&nbsp;</li>
+<li><a href="{{ pathto('contents') }}">contents</a> &raquo;</li>
+{% endblock %}
+

CGATPipelines/pipeline_docs/pipeline_rrbs/_templates/search.html

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+{% extends "layout.html" %}
+{% set title = _('Search') %}
+{% set script_files = script_files + ['_static/searchtools.js'] %}
+{% block body %}
+  <h1 id="search-documentation">{{ _('Search') }}</h1>
+  <p>
+    {% trans %}From here you can search these documents. Enter your
+    search words into the box below and click "search". Note that the
+    search function will automatically search for all of the
+    words. Pages containing less words won't appear in the result
+    list.{% endtrans %}  If you want to limit your search to working code examples,
+    include the keyword "codex" (mnemonic for <i>code example</i>) in your
+    search, eg "codex ellipse"; 
+    see <a href="{{ pathto('faq/howto_faq.html#search-examples') }}">search&nbsp;examples</a>.
+  </p>
+  <form action="" method="get">
+    <input type="text" name="q" value="" />
+    <input type="submit" value="{{ _('search') }}" />
+    <span id="search-progress" style="padding-left: 10px"></span>
+  </form>
+  {% if search_performed %}
+    <h2>{{ _('Search Results') }}</h2>
+    {% if not search_results %}
+      <p>{{ _('Your search did not match any results.') }}</p>
+    {% endif %}
+  {% endif %}
+  <div id="search-results">
+  {% if search_results %}
+    <ul>
+    {% for href, caption, context in search_results %}
+      <li><a href="{{ pathto(item.href) }}">{{ caption }}</a>
+        <div class="context">{{ context|e }}</div>
+      </li>
+    {% endfor %}
+    </ul>
+  {% endif %}
+  </div>
+{% endblock %}
+{% block footer %}
+  {{ super() }}
+  <script type="text/javascript" src="searchindex.js"></script>
+{% endblock %}

CGATPipelines/pipeline_docs/pipeline_rrbs/contents.rst

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+.. Test documentation master file, created by
+   sphinx-quickstart on Mon Mar 23 15:27:57 2009.
+
+==========
+ Contents
+==========
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   pipeline.rst
+
+
+

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline.rst

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+==============
+RRBS pipeline
+==============
+
+Contents:
+
+.. toctree::
+   :maxdepth: 4
+
+   pipeline/QC.rst
+   pipeline/Coverage.rst
+   pipeline/summaryPlots.rst
+   pipeline/summaryPlots/ReadPositionsMethylationBias.rst
+   pipeline/summaryPlots/MethylationBySample.rst
+   pipeline/summaryPlots/Heatmaps.rst
+
+.. errorlist::
+
+

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline/Coverage.rst

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+========
+Coverage
+========
+
+Coverage across CpGs
+==========================
+
+The following plot shows the frequency of CpGs for coverage values
+between 1-100.
+
+.. report:: Coverage.coverage
+   :render: r-ggplot
+   :transform: toframe
+   :statement: aes(x=cov,y=freq) +
+	       geom_line(size=1,aes(linetype=as.factor(rep), 
+	       colour=paste0(sample,'-',condition))) +
+	       geom_vline(linetype = "longdash", xintercept = 10) +
+	       coord_cartesian(ylim = c(0,80000), xlim = c(0,100)) +
+	       ylab('Frequency') +
+	       xlab('Coverage') +
+	       scale_linetype_discrete(name='Replicate') +
+	       scale_colour_discrete(name='Tissue - Treatment') +
+	       theme(axis.text.x=element_text(size=20),
+	       axis.title.x=element_text(size=20),
+	       axis.text.y=element_text(size=20),
+	       axis.title.y=element_text(size=20),
+	       title=element_text(size=20),
+	       legend.text=element_text(size=20))
+
+
+   The curves show the frequency of CpGs at the the coverage value
+   indicated on the x-axis. The y-axis has been trimmed such that the
+   frequency of CpGs with very low coverage is not plotted. 
+   The dashed black line represents a coverage threshold of 10X which is
+   frequently used for making methylation calls. Colours and line
+   types are used to indicate the samples and replicate number.
+
+
+
+The following plot shows the fraction of sequence reads which would
+remain across a range of coverage thresholds
+
+.. report:: Coverage.readsRemaining
+   :render: r-ggplot
+   :transform: toframe
+   :statement: aes(x=threshold,y=percentage,group=file) +
+	       geom_line(size=1,aes(linetype=as.factor(rep), 
+	       colour=paste0(sample,'-',condition))) + 
+	       geom_vline(linetype = "longdash", xintercept = 10) +
+	       coord_cartesian(xlim = c(0,100))+
+	       ylab('Fraction of sequencing remaining') + 
+	       xlab('Coverage threshold') + 
+	       scale_linetype_discrete(name='Replicate') +   
+	       scale_colour_discrete(name='Tissue - Treatment') + 
+	       theme(axis.text.x=element_text(size=20),
+	       axis.title.x=element_text(size=20),
+	       axis.text.y=element_text(size=20),
+	       axis.title.y=element_text(size=20), 
+	       title=element_text(size=20),
+	       legend.text=element_text(size=20))
+
+
+   The curves show the fraction of mapped reads which remain using the
+   coverage value indicated on the x-axis. 
+   The dashed black line represents a coverage threshold of 10X which
+   is frequently used for making methylation calls. Colours and line
+   types are used to indicate the samples and replicate number.
+
+
+
+
+The following plot shows the number of CpGs which overlap at 10X coverage
+
+.. report:: Coverage.CpGOverlap
+   :render: r-ggplot
+   :transform: toframe
+   :statement: aes(x=overlaps,y=CpGs) +
+	       geom_bar(stat="identity")+ 
+	       ylab('Number of CpGs') +
+	       xlab('Number of samples') +
+	       theme(axis.text.x=element_text(size=20),
+	       axis.title.x=element_text(size=20),
+	       axis.text.y=element_text(size=20),
+	       axis.title.y=element_text(size=20), 
+	       title=element_text(size=20),
+	       legend.text=element_text(size=20))+
+	       scale_x_continuous(breaks=seq(1,1000,1))
+
+
+   The bars represent the number of CpGs which overlap at 10X coverage
+   for the number of samples indicated on the x-axis.