Commit 0c4e2c5a authored by Christian Arnold's avatar Christian Arnold
Browse files

GRaNIE: New version, added TF enrichment

parent b09d24c1
Pipeline #28197 passed with stage
in 20 seconds
Package: GRaNIE
Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Version: 0.14.3
Version: 0.14.4
Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")),
......
......@@ -4280,6 +4280,13 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"),
background = "neighborhood",
clustering = "louvain",
communities = seq_len(10), display = "byRank",
TF_rankType = "degree",
TF_topNodes_n = 0.1,
TF_names = NULL,
TF_plot_topn_pvalue = 30,
TF_plot_p = 0.05,
TF_plot_nSignificant = 3,
TF_plot_nGO = 10,
outputFolder = NULL,
forceRerun = FALSE) {
......@@ -4303,6 +4310,17 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"),
GRN = plotCommunitiesEnrichment(GRN, outputFolder = outputFolder, display = display, communities = communities, forceRerun = forceRerun)
GRN = calculateTFEnrichment(GRN, rankType = TF_rankType, n = TF_topNodes_n, TF.names = TF_names,
ontology = ontology, algorithm = algorithm,
statistic = statistic, background = background,
forceRerun = forceRerun)
GRN = plotTFEnrichment(GRN, rankType = TF_rankType, n = TF_topNodes_n, TF.names = TF_names,
topn_pvalue = TF_plot_topn_pvalue, p = TF_plot_p,
nSignificant = TF_plot_nSignificant, nGO = TF_plot_nGO,
outputFolder = outputFolder, forceRerun = forceRerun)
.printExecutionTime(start)
......@@ -4687,7 +4705,7 @@ calculateCommunitiesEnrichment <- function(GRN,
communitiesDisplay = stats::na.omit(communitiesCount$community[communities])
}
futile.logger::flog.info(paste0("Running enrichment analysis for all communities. This may take a while..."))
futile.logger::flog.info(paste0("Running enrichment analysis for all ", length(communitiesDisplay)," communities. This may take a while..."))
mapping = .getGenomeObject(GRN@config$parameters$genomeAssembly, type = "packageName")
......
......@@ -2599,7 +2599,7 @@ plotTFEnrichment <- function(GRN, rankType = "degree", n = 0.1, TF.names = NULL,
}
# plot the comparative heatmap:
for (ontology in names(purrr::transpose(purrr::transpose(GRN@stats$Enrichment[["byTF"]])$results))){
for (ontologyCur in names(purrr::transpose(purrr::transpose(GRN@stats$Enrichment[["byTF"]])$results))){
enrichmentData = purrr::transpose(purrr::transpose(GRN@stats$Enrichment[["byTF"]])$results)[[ontologyCur]][TFset]
......
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......@@ -86,13 +84,13 @@
</header><div class="row">
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<h1 data-toc-skip>Get Started with the <em>GRaNIE</em> packages from the Zaugg Lab</h1>
<h4 data-toc-skip class="author">Christian Arnold, Judith Zaugg</h4>
<h4 class="author">Christian Arnold, Judith Zaugg</h4>
<h4 data-toc-skip class="date">15 December 2021</h4>
<h4 class="date">18 December 2021</h4>
<div class="hidden name"><code>quickStart.Rmd</code></div>
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<p><strong>This vignette gives you a 1 minute summary of how to install and use our <em>GRaNIE</em> packages. For more details, check out the other Vignettes.</strong></p>
<div class="section level2">
<h2 id="install-the-packages">Install the packages<a class="anchor" aria-label="anchor" href="#install-the-packages"></a>
</h2>
<div class="section level3">
<h3 id="stable-version-granie">Stable version: <em>GRaNIE</em><a class="anchor" aria-label="anchor" href="#stable-version-granie"></a>
<div id="install-the-packages" class="section level2">
<h2 class="hasAnchor">
<a href="#install-the-packages" class="anchor"></a>Install the packages</h2>
<div id="stable-version-granie" class="section level3">
<h3 class="hasAnchor">
<a href="#stable-version-granie" class="anchor"></a>Stable version: <em>GRaNIE</em>
</h3>
<p>Installing our <em>GRaNIE</em> packages is easy. Just execute the following line into <em>R</em>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/" class="external-link">devtools</a></span><span class="op">)</span>
<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIE"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/">devtools</a></span><span class="op">)</span>
<span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIE"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>If you receive an error message, make sure you installed the devtools package. If you don’t have it installed yet, just execute the following code into <em>R</em>:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level3">
<h3 id="development-version-graniedev">Development version: <em>GRaNIEdev</em><a class="anchor" aria-label="anchor" href="#development-version-graniedev"></a>
<div id="development-version-graniedev" class="section level3">
<h3 class="hasAnchor">
<a href="#development-version-graniedev" class="anchor"></a>Development version: <em>GRaNIEdev</em>
</h3>
<p>To install the development version of our <em>GRN</em> package, simply do:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEdev"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEdev"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
</div>
<div class="section level3">
<h3 id="data-package-graniedata">Data package: <em>GRaNIEData</em><a class="anchor" aria-label="anchor" href="#data-package-graniedata"></a>
<div id="data-package-graniedata" class="section level3">
<h3 class="hasAnchor">
<a href="#data-package-graniedata" class="anchor"></a>Data package: <em>GRaNIEData</em>
</h3>
<p>Similarly, to install the <em>GRaNIEData</em> package, simply do:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html" class="external-link">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEData"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org/reference/remote-reexports.html">install_gitlab</a></span><span class="op">(</span><span class="st">"grp-zaugg/GRaNIE"</span>, subdir <span class="op">=</span> <span class="st">"src/GRaNIEData"</span>, host <span class="op">=</span> <span class="st">"git.embl.de"</span>, force <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
</div>
</div>
<div class="section level2">
<h2 id="what-do-the-different-packages-do">What do the different packages do?<a class="anchor" aria-label="anchor" href="#what-do-the-different-packages-do"></a>
</h2>
<div id="what-do-the-different-packages-do" class="section level2">
<h2 class="hasAnchor">
<a href="#what-do-the-different-packages-do" class="anchor"></a>What do the different packages do?</h2>
<p>The stable version <strong><em>GRaNIE</em></strong> package is the best choice for most users, it contains features that have been tested more thoroughly and that we provide support for.</p>
<p>The development version <strong><em>GRaNIEdev</em></strong> contains new features that may or may not be tested so far and we can only provide limited support for it. This is the version we actively work on, and every once in a while after finishing a new feature, we integrate it into the stable version in the <em>GRaNIE</em> package.</p>
<p>The <strong><em>GRaNIEdata</em></strong> package provides example data that can be used to test the package and run the Vignettes.</p>
</div>
<div class="section level2">
<h2 id="bug-reports-feature-requests-and-contact-information">Bug Reports, Feature Requests and Contact Information<a class="anchor" aria-label="anchor" href="#bug-reports-feature-requests-and-contact-information"></a>
</h2>
<p>Please check out <strong><a href="https://grp-zaugg.embl-community.io/GRaNIE" class="external-link">https://grp-zaugg.embl-community.io/GRaNIE</a></strong> for how to get in contact with us.</p>
<div id="bug-reports-feature-requests-and-contact-information" class="section level2">
<h2 class="hasAnchor">
<a href="#bug-reports-feature-requests-and-contact-information" class="anchor"></a>Bug Reports, Feature Requests and Contact Information</h2>
<p>Please check out <strong><a href="https://grp-zaugg.embl-community.io/GRaNIE">https://grp-zaugg.embl-community.io/GRaNIE</a></strong> for how to get in contact with us.</p>
</div>
</div>
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<p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
<p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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