bugfix for modulepreservation and updates to tutorials

smorabit · Mar 8, 2024 · b3b5acf · b3b5acf
1 parent 985d90a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hdWGCNA
 Title: hdWGCNA
-Version: 0.3.00
+Version: 0.3.01
 Authors@R: c(
     person("Sam", "Morabito", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7768-4856")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# hdWGCNA 0.3.01 (2024-03-07)
+## Added
+- None
+
+## Changes
+- Bugfix in `ModulePreservation`
+- Update to module preservation tutorial and project modules tutorial.
+
 # hdWGCNA 0.3.00 (2024-02-27)
 ## Added
 - First version with support for Seurat v5.

diff --git a/R/ModulePreservation.R b/R/ModulePreservation.R
@@ -49,13 +49,19 @@ ModulePreservation <- function(
     colnames(datExpr_query)  <- gene_mapping[,genome1_col]
   }
 
+  genes_keep <- intersect(colnames(datExpr_ref), colnames(datExpr_query))
+  datExpr_ref <- datExpr_ref[,genes_keep]
+  datExpr_query <- datExpr_query[,genes_keep]
+
   # set up multiExpr:
   setLabels <- c("ref", "query")
   multiExpr <- list(
     ref = list(data=datExpr_ref),
     query = list(data=datExpr_query)
   )
-  ref_modules <- list(ref = GetModules(seurat_ref, wgcna_name=wgcna_name)$module)
+  ref_modules <- GetModules(seurat_ref, wgcna_name=wgcna_name_ref)
+  ref_modules <- ref_modules[genes_keep,]
+  ref_modules <- list(ref = ref_modules$module)
 
   # print('ref:')
   # print(dim(multiExpr$ref$data))

diff --git a/R/ProjectModules.R b/R/ProjectModules.R
@@ -35,6 +35,7 @@ ProjectModules <- function(
 
   # get data from active assay if wgcna_name is not given
   if(is.null(wgcna_name)){wgcna_name <- seurat_ref@misc$active_wgcna}
+  CheckWGCNAName(seurat_ref, wgcna_name)
 
   # get modules to be projected:
   if(is.null(modules)){

diff --git a/R/plotting.R b/R/plotting.R
@@ -1725,8 +1725,6 @@ DoHubGeneHeatmap <- function(
 #' @param wgcna_name The name of the hdWGCNA experiment in the seurat_obj@misc slot
 #' @keywords scRNA-seq
 #' @export
-#' @examples
-#' PlotModulePreservation
 PlotModulePreservation <- function(
   seurat_obj,
   name,
@@ -1847,8 +1845,6 @@ PlotModulePreservation <- function(
 #' @param combine logical determining whether to plot as one combined plot (TRUE) or to return individual plots as a list (FALSE)
 #' @keywords scRNA-seq
 #' @export
-#' @examples
-#' PlotModulePreservation
 PlotModuleTraitCorrelation <- function(
   seurat_obj,
   high_color = 'red',

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/ST_basics.html b/docs/articles/ST_basics.html
diff --git a/docs/articles/basic_tutorial.html b/docs/articles/basic_tutorial.html
diff --git a/docs/articles/consensus_wgcna.html b/docs/articles/consensus_wgcna.html
diff --git a/docs/articles/customization.html b/docs/articles/customization.html
diff --git a/docs/articles/differential_MEs.html b/docs/articles/differential_MEs.html
diff --git a/docs/articles/enrichment_analysis.html b/docs/articles/enrichment_analysis.html
diff --git a/docs/articles/figures/.DS_Store b/docs/articles/figures/.DS_Store
diff --git a/docs/articles/figures/projection/compare_umaps.png b/docs/articles/figures/projection/compare_umaps.png
diff --git a/docs/articles/figures/projection/module_preservation_all.png b/docs/articles/figures/projection/module_preservation_all.png
diff --git a/docs/articles/figures/projection/module_preservation_rank.png b/docs/articles/figures/projection/module_preservation_rank.png
diff --git a/docs/articles/figures/projection/module_preservation_summary.png b/docs/articles/figures/projection/module_preservation_summary.png
diff --git a/docs/articles/figures/projection/projected_dotplot.png b/docs/articles/figures/projection/projected_dotplot.png
diff --git a/docs/articles/figures/projection/projected_featureplots.png b/docs/articles/figures/projection/projected_featureplots.png
diff --git a/docs/articles/hdWGCNA.html b/docs/articles/hdWGCNA.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/isoform_pbmcs.html b/docs/articles/isoform_pbmcs.html