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 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")),
......
...@@ -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")
......
...@@ -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]
......
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<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>
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<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>
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<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>
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<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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