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Commit 0c4e2c5a authored by Christian Arnold's avatar Christian Arnold
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GRaNIE: New version, added TF enrichment

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src/GRaNIE/DESCRIPTION
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Package: GRaNIE Package: GRaNIE
Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data 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 Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email = Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")), "christian.arnold@embl.de", role = c("cre","aut")),
......
src/GRaNIE/R/core.R
View file @ 0c4e2c5a
...@@ -4280,6 +4280,13 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"), ...@@ -4280,6 +4280,13 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"),
background = "neighborhood", background = "neighborhood",
clustering = "louvain", clustering = "louvain",
communities = seq_len(10), display = "byRank", 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, outputFolder = NULL,
forceRerun = FALSE) { forceRerun = FALSE) {
...@@ -4303,6 +4310,17 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"), ...@@ -4303,6 +4310,17 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"),
GRN = plotCommunitiesEnrichment(GRN, outputFolder = outputFolder, display = display, communities = communities, forceRerun = forceRerun) 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) .printExecutionTime(start)
...@@ -4687,7 +4705,7 @@ calculateCommunitiesEnrichment <- function(GRN, ...@@ -4687,7 +4705,7 @@ calculateCommunitiesEnrichment <- function(GRN,
communitiesDisplay = stats::na.omit(communitiesCount$community[communities]) communitiesDisplay = stats::na.omit(communitiesCount$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") mapping = .getGenomeObject(GRN@config$parameters$genomeAssembly, type = "packageName")
......
src/GRaNIE/R/plot.R
View file @ 0c4e2c5a
...@@ -2599,7 +2599,7 @@ plotTFEnrichment <- function(GRN, rankType = "degree", n = 0.1, TF.names = NULL, ...@@ -2599,7 +2599,7 @@ plotTFEnrichment <- function(GRN, rankType = "degree", n = 0.1, TF.names = NULL,
} }
# plot the comparative heatmap: # 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] enrichmentData = purrr::transpose(purrr::transpose(GRN@stats$Enrichment[["byTF"]])$results)[[ontologyCur]][TFset]
......
src/GRaNIE/docs/404.html
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...@@ -38,13 +81,13 @@ ...@@ -38,13 +81,13 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">GRaNIE</a> <a class="navbar-link" href="index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.14.4</span>
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...@@ -57,7 +100,7 @@ ...@@ -57,7 +100,7 @@
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<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
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<a href="articles/quickStart.html">Getting Started</a> <a href="articles/quickStart.html">Getting Started</a>
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...@@ -75,17 +118,19 @@ ...@@ -75,17 +118,19 @@
<a href="news/index.html">Changelog &amp; News</a> <a href="news/index.html">Changelog &amp; News</a>
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<h1>Page not found (404)</h1> <h1>Page not found (404)</h1>
...@@ -96,31 +141,31 @@ Content not found. Please use links in the navbar. ...@@ -96,31 +141,31 @@ Content not found. Please use links in the navbar.
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src/GRaNIE/docs/articles/Introduction.html
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src/GRaNIE/docs/articles/index.html
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...@@ -40,7 +99,8 @@ ...@@ -40,7 +99,8 @@
<span class="caret"></span> <span class="caret"></span>
</a> </a>
<ul class="dropdown-menu" role="menu"><li> <ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/quickStart.html">Getting Started</a> <a href="../articles/quickStart.html">Getting Started</a>
</li> </li>
<li> <li>
...@@ -49,20 +109,28 @@ ...@@ -49,20 +109,28 @@
<li> <li>
<a href="../articles/workflow.html">Workflow example</a> <a href="../articles/workflow.html">Workflow example</a>
</li> </li>
</ul></li> </ul>
</li>
<li> <li>
<a href="../reference/index.html">Reference</a> <a href="../reference/index.html">Reference</a>
</li> </li>
<li> <li>
<a href="../news/index.html">Changelog &amp; News</a> <a href="../news/index.html">Changelog &amp; News</a>
</li> </li>
</ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container --> </div><!--/.container -->
</div><!--/.navbar --> </div><!--/.navbar -->
</header><div class="row"> </header>
<div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header"> <div class="page-header">
<h1>Articles</h1> <h1>Articles</h1>
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<div class="section "> <div class="section ">
<h3>Getting started</h3> <h3>Getting started</h3>
<p class="section-desc"></p><p>Getting started in 1 minute</p> <p class="section-desc"><p>Getting started in 1 minute</p></p>
<dl><dt><a href="quickStart.html">Get Started with the *GRaNIE* packages from the Zaugg Lab</a></dt> <dl>
<dd> <dt><a href="quickStart.html">Get Started with the *GRaNIE* packages from the Zaugg Lab</a></dt>
</dd></dl></div> <dd></dt>
</dl>
</div>
<div class="section "> <div class="section ">
<h3>Introduction</h3> <h3>Introduction</h3>
<p class="section-desc"></p><p>Learn what the GRaNIE package is and what you can use it for</p> <p class="section-desc"><p>Learn what the GRaNIE package is and what you can use it for</p></p>
<dl><dt><a href="Introduction.html">Introduction and Methodological Details</a></dt> <dl>
<dd> <dt><a href="Introduction.html">Introduction and Methodological Details</a></dt>
</dd></dl></div> <dd></dt>
</dl>
</div>
<div class="section "> <div class="section ">
<h3>Workflow example</h3> <h3>Workflow example</h3>
<p class="section-desc"></p><p>Learn how to use the GRaNIE package with a full workflow example</p> <p class="section-desc"><p>Learn how to use the GRaNIE package with a full workflow example</p></p>
<dl><dt><a href="workflow.html">Workflow example</a></dt> <dl>
<dd> <dt><a href="workflow.html">Workflow example</a></dt>
</dd></dl></div> <dd></dt>
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<p></p><p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p> <div class="copyright">
<p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
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<p></p><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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src/GRaNIE/docs/articles/quickStart.html
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</script> </script>
</head> </head>
<body data-spy="scroll" data-target="#toc"> <body data-spy="scroll" data-target="#toc">
<div class="container template-article"> <div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
...@@ -39,7 +37,7 @@ ...@@ -39,7 +37,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">GRaNIE</a> <a class="navbar-link" href="../index.html">GRaNIE</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.3</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.14.4</span>
</span> </span>
</div> </div>
...@@ -86,13 +84,13 @@ ...@@ -86,13 +84,13 @@