Minor documentation updates

- Bioconductor 3.9 - New function: add_cellAnnotation for looms
aertslab · May 31, 2019 · 0a4c96e · 0a4c96e
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,4 +2,14 @@
 ^\.Rproj\.user$
 .gitignore
 .Rhistory
-.Rbuildignore
+.DS_Store
+.DS_Store?
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+packrat/lib*/
+packrat/src/
+z_*
+vignettes/SCENIC_MouseBrain
+vignettes/pySCENIC_tutorial
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,7 @@
-SCENIC.Rproj
 .gitignore
 .Rproj.user
 .Rhistory
+.Rbuildignore
 .Rprofile
 .RData
 .Ruserdata
@@ -15,4 +15,6 @@ Thumbs.db
 packrat/lib*/
 packrat/src/
 z_*
-vignettes/SCENIC_MouseBrain/
+vignettes/SCENIC_MouseBrain
+vignettes/pySCENIC_tutorial
+SCENIC.Rproj
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SCENIC
 Type: Package
 Title: SCENIC (Single Cell rEgulatory Network Inference and Clustering)
-Version: 1.1.1-10
-Date: 2019-04-22
+Version: 1.1.2-01
+Date: 2019-05-31
 Author: Sara Aibar, Carmen Bravo, Stein Aerts. 
   Laboratory of Computational Biology, KU Leuven Center for Human Genetics. 
   Leuven, Belgium.

diff --git a/NAMESPACE b/NAMESPACE
@@ -47,5 +47,6 @@ exportMethods(getSettings)
 exportMethods(loadFile)
 exportMethods(loadInt)
 import(AUCell)
+import(SingleCellExperiment)
 import(data.table)
 importFrom(R.utils,capitalize)
diff --git a/R/add_cellAnnotation.R b/R/add_cellAnnotation.R
@@ -0,0 +1,41 @@
+
+#' @import SingleCellExperiment
+#' @import SingleCellExperiment
+load_as_sce <- function(loomPath)
+{
+  loom <- open_loom(loomPath, mode="r")
+  dgem <- get_dgem(loom)
+  cellAnnot <- get_cellAnnotation(loom)
+  embeddings <- get_embeddings(loom)
+  close_loom(loom)
+
+  sce <- SingleCellExperiment::SingleCellExperiment(assays=list(counts=dgem),
+                                                    colData=data.frame(cellAnnot[colnames(dgem),, drop=FALSE]),
+                                                    reducedDims=S4Vectors::SimpleList(embeddings))
+
+  return(sce)
+}
+
+
+add_cellAnnotation <- function(loom, cellAnnotation)
+{
+  cellAnnotation <- data.frame(cellAnnotation)
+  if(any(c("nGene", "nUMI") %in% colnames(cellAnnotation)))
+  {
+    warning("Columns 'nGene' and 'nUMI' will not be added as annotations to the loom file.")
+    cellAnnotation <- cellAnnotation[,colnames(cellAnnotation) != "nGene", drop=FALSE]
+    cellAnnotation <- cellAnnotation[,colnames(cellAnnotation) != "nUMI", drop=FALSE]
+  }
+
+  if(ncol(cellAnnotation)<=0) stop("The cell annotation contains no columns")
+  if(!all(get_cell_ids(loom) %in% rownames(cellAnnotation))) stop("Cell IDs are missing in the annotation")
+
+  cellAnnotation <- cellAnnotation[get_cell_ids(loom),,drop=FALSE]
+  # Add annotation
+  for(cn in colnames(cellAnnotation))
+  {
+    add_col_attr(loom=loom, key=cn, value=cellAnnotation[,cn])
+  }
+
+  invisible(loom)
+}
diff --git a/R/aux_export2scope.R b/R/aux_export2scope.R
@@ -72,6 +72,12 @@ export2scope <- function(scenicOptions, dgem, hierarchy=c("SCENIC", "", ""), add
   motifEnrichment <- loadInt(scenicOptions, "motifEnrichment_selfMotifs_wGenes")
   motifEnrichment <- motifEnrichment[grep("transfac_pro__", motifEnrichment[["motif"]], invert = T),] #TODO
   regulonThresholds <- loadInt(scenicOptions, "aucell_thresholds")
+  if(!"aucThr" %in% names(regulonThresholds[[1]]))
+  {
+    # regulonThresholds <- lapply(regulonThresholds, function(x) list(selected=x))
+    warning("The binarized regulon activity will not been added to the loom.")
+    regulonThresholds <- NULL
+  }
   add_scenic_regulons(loom=loom
                       , regulons=regulons
                       , regulon.threshold.assignments=regulonThresholds # Optional

diff --git a/inst/doc/SCENIC_Running.html b/inst/doc/SCENIC_Running.html
diff --git a/inst/doc/SCENIC_Setup.html b/inst/doc/SCENIC_Setup.html
diff --git a/inst/doc/detailedStep_0_geneFilter.html b/inst/doc/detailedStep_0_geneFilter.html
@@ -10,6 +10,7 @@
 
 
 
+<meta name="date" content="2019-05-31" />
 
 <title>Code of geneFiltering()</title>
 
@@ -93,81 +94,17 @@
 button.code-folding-btn:focus {
   outline: none;
 }
-summary {
-  display: list-item;
-}
 </style>
 
 
 
 <div class="container-fluid main-container">
 
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-
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-    $(this).parent().toggleClass('nav-tabs-open')
-  });
-});
 </script>
 
 <!-- code folding -->
@@ -176,15 +113,16 @@
 
 
 
+
 <div class="fluid-row" id="header">
 
 
 
 <h1 class="title toc-ignore">Code of geneFiltering()</h1>
 <h3 class="subtitle"><em>Workflow run by geneFiltering()</em></h3>
-<h4 class="date"><em>7 February 2019</em></h4>
+<h4 class="date"><em>31 May 2019</em></h4>
 <h4 class="package">Package</h4>
-<p>SCENIC 1.1.1.9</p>
+<p>SCENIC 1.1.2.1</p>
 
 </div>
 

diff --git a/inst/doc/detailedStep_1_coexNetwork2modules.html b/inst/doc/detailedStep_1_coexNetwork2modules.html
@@ -10,6 +10,7 @@
 
 
 
+<meta name="date" content="2019-05-31" />
 
 <title>Code of runSCENIC_1_coexNetwork2modules()</title>
 
@@ -93,81 +94,17 @@
 button.code-folding-btn:focus {
   outline: none;
 }
-summary {
-  display: list-item;
-}
 </style>
 
 
 
 <div class="container-fluid main-container">
 
 <!-- tabsets -->
-
-<style type="text/css">
-.tabset-dropdown > .nav-tabs {
-  display: inline-table;
-  max-height: 500px;
-  min-height: 44px;
-  overflow-y: auto;
-  background: white;
-  border: 1px solid #ddd;
-  border-radius: 4px;
-}
-
-.tabset-dropdown > .nav-tabs > li.active:before {
-  content: "";
-  font-family: 'Glyphicons Halflings';
-  display: inline-block;
-  padding: 10px;
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-}
-
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-  display: block;
-  float: none;
-}
-
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-  display: none;
-}
-</style>
-
 <script>
 $(document).ready(function () {
   window.buildTabsets("TOC");
 });
-
-$(document).ready(function () {
-  $('.tabset-dropdown > .nav-tabs > li').click(function () {
-    $(this).parent().toggleClass('nav-tabs-open')
-  });
-});
 </script>
 
 <!-- code folding -->
@@ -176,15 +113,16 @@
 
 
 
+
 <div class="fluid-row" id="header">
 
 
 
 <h1 class="title toc-ignore">Code of runSCENIC_1_coexNetwork2modules()</h1>
 <h3 class="subtitle"><em>Workflow run by runSCENIC_1_coexNetwork2modules()</em></h3>
-<h4 class="date"><em>7 February 2019</em></h4>
+<h4 class="date"><em>31 May 2019</em></h4>
 <h4 class="package">Package</h4>
-<p>SCENIC 1.1.1.9</p>
+<p>SCENIC 1.1.2.1</p>
 
 </div>