working on new tutorial (81f9fd13) · Commits · github_fork / HdWGCNA

R/getters_and_setters.R

+9 −7

Original line number	Diff line number	Diff line
		@@ -204,6 +204,9 @@ SetDatExpr <- function(
		s_obj <- seurat_obj
		}

		# get the metadata from the seurat object:
		seurat_meta <- s_obj@meta.data


		if(is.null(assay)){
		assay <- DefaultAssay(s_obj)
		@@ -216,14 +219,13 @@ SetDatExpr <- function(
		}

		# check that group.by is in the Seurat object & in the metacell object:
		if(!is.null(group.by)){
		if(!(group.by %in% colnames(s_obj@meta.data))){
		m_cell_message <- ""
		if(use_metacells){m_cell_message <- "metacell"}
		stop(paste0(group.by, ' not found in the meta data of the ', m_cell_message, ' Seurat object'))
		}

		# get the metadata from the seurat object:
		seurat_meta <- s_obj@meta.data
		}

		# columns to group by for cluster/celltype
		if(!is.null(group.by)){

+2 −0

Original line number	Diff line number	Diff line
		@@ -56,6 +56,8 @@ navbar:
		href: articles/consensus_wgcna.html
		- text: Motif analysis
		href: articles/motif_analysis.html
		- text: Alternative metacell algorithms
		href: articles/other_metacells.html
		- text: -------
		- text: Other
		- text: Module customization

+3 −0

Original line number	Diff line number	Diff line
		@@ -92,6 +92,9 @@
		<li>
		<a href="https://smorabit.github.io/hdWGCNA/articles/motif_analysis.html">Motif analysis</a>
		</li>
		<li>
		<a href="https://smorabit.github.io/hdWGCNA/articles/other_metacells.html">Alternative metacell algorithms</a>
		</li>
		<li class="divider">
		</li>
		<li class="dropdown-header">Other</li>

+3 −0

Original line number	Diff line number	Diff line
		@@ -65,6 +65,9 @@
		<li>
		<a href="articles/motif_analysis.html">Motif analysis</a>
		</li>
		<li>
		<a href="articles/other_metacells.html">Alternative metacell algorithms</a>
		</li>
		<li class="divider">
		<li class="dropdown-header">Other</li>
		<li>

+3 −0

Original line number	Diff line number	Diff line
		@@ -65,6 +65,9 @@
		<li>
		<a href="articles/motif_analysis.html">Motif analysis</a>
		</li>
		<li>
		<a href="articles/other_metacells.html">Alternative metacell algorithms</a>
		</li>
		<li class="divider">
		<li class="dropdown-header">Other</li>
		<li>