Commit fabc6fe6 authored by smorabit's avatar smorabit
Browse files

adding in functinos that accidently got removed

parent e09b2bdb

NAMESPACE

+6 −0
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ 
export(AvgModuleExpr)

export(ConstructMetacells)

export(ConstructMetaspots)

export(DimPlotMetacells)

export(DoHubGeneHeatmap)

export(EnrichrBarPlot)

export(EnrichrDotPlot)
@@ -49,6 +50,7 @@ export(ModuleUMAPPlot) 
export(MotifOverlapBarPlot)

export(MotifScan)

export(MotifTargetScore)

export(NormalizeMetacells)

export(OverlapBarPlot)

export(OverlapDotPlot)

export(OverlapModulesDEGs)
@@ -64,7 +66,11 @@ export(ROCCurves) 
export(ResetModuleColors)

export(ResetModuleNames)

export(RunEnrichr)

export(RunHarmonyMetacells)

export(RunModuleUMAP)

export(RunPCAMetacells)

export(RunUMAPMetacells)

export(ScaleMetacells)

export(SelectNetworkGenes)

export(SetActiveWGCNA)

export(SetAvgModuleExpr)

R/metacells.R

+6 −2
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@@ -234,9 +234,7 @@ ConstructMetacells <- function( 
#' @param max_iter the maximum number of iterations in the metacells bootstrapping loop

#' @param verbose logical indicating whether to print additional information

#' @param wgcna_name name of the WGCNA experiment

#' @keywords scRNA-seq

#' @export

#' @examples

#' MetacellsByGroups

MetacellsByGroups <- function(

  seurat_obj, group.by=c('seurat_clusters'),
@@ -396,6 +394,7 @@ MetacellsByGroups <- function( 
#' Wrapper function to run Seurat's NormalizeData function on the metacell object.

#'

#' @param seurat_obj A Seurat object

#' @export

NormalizeMetacells <- function(seurat_obj, wgcna_name=NULL, ...){

  metacell_obj <- GetMetacellObject(seurat_obj, wgcna_name)

  metacell_obj <- Seurat::NormalizeData(metacell_obj, ...)
@@ -407,6 +406,7 @@ NormalizeMetacells <- function(seurat_obj, wgcna_name=NULL, ...){ 
#' Wrapper function to run Seurat's ScaleData function on the metacell object.

#'

#' @param seurat_obj A Seurat object

#' @export

ScaleMetacells <- function(seurat_obj, wgcna_name=NULL, ...){

  if(!exists("features")){

    features = VariableFeatures(seurat_obj)
@@ -421,6 +421,7 @@ ScaleMetacells <- function(seurat_obj, wgcna_name=NULL, ...){ 
#' Wrapper function to run Seurat's RunPCA function on the metacell object.

#'

#' @param seurat_obj A Seurat object

#' @export

RunPCAMetacells <- function(seurat_obj, wgcna_name=NULL, ...){

  metacell_obj <- GetMetacellObject(seurat_obj, wgcna_name)

  metacell_obj <- Seurat::RunPCA(metacell_obj, ...)
@@ -432,6 +433,7 @@ RunPCAMetacells <- function(seurat_obj, wgcna_name=NULL, ...){ 
#' Wrapper function to run harmony's RunHarmony function on the metacell object.

#'

#' @param seurat_obj A Seurat object

#' @export

RunHarmonyMetacells <- function(seurat_obj, ...){

  seurat_obj@misc[[seurat_obj@misc$active_wgcna]]$wgcna_metacell_obj <- harmony::RunHarmony(seurat_obj@misc[[seurat_obj@misc$active_wgcna]]$wgcna_metacell_obj, ...)

  seurat_obj
@@ -443,6 +445,7 @@ RunHarmonyMetacells <- function(seurat_obj, ...){ 
#'

#' @param seurat_obj A Seurat object

#' @keywords scRNA-seq

#' @export

RunUMAPMetacells <- function(seurat_obj, ...){

  seurat_obj@misc[[seurat_obj@misc$active_wgcna]]$wgcna_metacell_obj <- Seurat::RunUMAP(seurat_obj@misc[[seurat_obj@misc$active_wgcna]]$wgcna_metacell_obj, ...)

  seurat_obj
@@ -455,6 +458,7 @@ RunUMAPMetacells <- function(seurat_obj, ...){ 
#'

#' @param seurat_obj A Seurat object

#' @keywords scRNA-seq

#' @export

DimPlotMetacells <- function(seurat_obj, ...){

  Seurat::DimPlot(seurat_obj@misc[[seurat_obj@misc$active_wgcna]]$wgcna_metacell_obj, ...)

}

docs/pkgdown.yml

+1 −1
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@@ -17,7 +17,7 @@ articles: 
  projecting_modules: projecting_modules.html

  projecting_modules_cross: projecting_modules_cross.html

  sctransform: sctransform.html

last_built: 2023-01-25T05:59Z

last_built: 2023-01-25T22:03Z

urls:

  reference: https://smorabit.github.io/hdWGCNA/reference

  article: https://smorabit.github.io/hdWGCNA/articles

docs/reference/ConstructMetacells.html

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@@ -295,7 +295,7 @@ on neighboring cells.</p> 
<span class="r-out co"><span class="r-pr">#&gt;</span>     }</span>

<span class="r-out co"><span class="r-pr">#&gt;</span>     out</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x7fd88baf0ab0&gt;</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x7fcdad94f928&gt;</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:hdWGCNA&gt;</span>

</code></pre></div>

    </div>

docs/reference/DoHubGeneHeatmap.html

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@@ -233,7 +233,7 @@ using Seurat's DoHeatmap, and then assembles them all into one big heatmap.</p> 
<span class="r-out co"><span class="r-pr">#&gt;</span>     }</span>

<span class="r-out co"><span class="r-pr">#&gt;</span>     out</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x7fd88fd73c90&gt;</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x7fcdb4c1f778&gt;</span>

<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:hdWGCNA&gt;</span>

</code></pre></div>

    </div>

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