docs for metaspot funcs

export(ComputeModuleEigengene)

export(ComputeROC)

export(ConstructMetacells)

export(ConstructMetaspots)

export(ConstructNetwork)

export(DimPlotMetacells)

export(DoHubGeneHeatmap)

export(GetWGCNAParams)

export(HubGeneNetworkPlot)

export(MetacellsByGroups)

export(MetaspotsByGroups)

export(ModuleConnectivity)

export(ModuleCorrNetwork)

export(ModuleCorrelogram)

#' This function is called by MetaspotsByGroups and should NOT be run directly!

#' @param cur_seurat A Seurat object

#' @param mode "sum" or "average"

#' @param

#' @param

#' @param assay Assay to extract data for aggregation. Default = 'Spatial'

#' @param slot Slot to extract data for aggregation. Default = 'counts'

#' @keywords ST

#' @export

#' @examples

#'

#' @param cur_seurat A Seurat object

#' @param group.by A character vector of Seurat metadata column names representing groups for which metacells will be computed.

#' @param assay Assay to extract data for aggregation. Default = 'RNA'

#' @param slot Slot to extract data for aggregation. Default = 'data'

#' @param assay Assay to extract data for aggregation. Default = 'Spatial'

#' @param slot Slot to extract data for aggregation. Default = 'counts'

#' @param mode determines how to make gene expression profiles for metacells from their constituent single cells. Options are "average" or "sum".

#' @param wgcna_name name of the WGCNA experiment

#' @keywords ST

#' @param name A string appended to resulting metalcells. Default = 'agg'

#' @param reduction A dimensionality reduction stored in the Seurat object. Default = 'umap'

#' @param assay Assay to extract data for aggregation. Default = 'RNA'

#' @param slot Slot to extract data for aggregation. Default = 'data'

#' @param slot Slot to extract data for aggregation. Default = 'counts'

#' @param return_metacell Logical to determine if we return the metacell seurat object (TRUE), or add it to the misc in the original Seurat object (FALSE). Default to FALSE.

#' @param mode determines how to make gene expression profiles for metacells from their constituent single cells. Options are "average" or "sum".

#' @param max_shared the maximum number of cells to be shared across two metacells

#' @param name A string appended to resulting metalcells. Default = 'agg'

#' @param reduction A dimensionality reduction stored in the Seurat object. Default = 'pca'

#' @param assay Assay to extract data for aggregation. Default = 'RNA'

#' @param slot Slot to extract data for aggregation. Default = 'data'

#' @param slot Slot to extract data for aggregation. Default = 'counts'

#' @param mode determines how to make gene expression profiles for metacells from their constituent single cells. Options are "average" or "sum".

#' @param min_cells the minimum number of cells in a particular grouping to construct metacells

#' @param max_shared the maximum number of cells to be shared across two metacells

<span class="op">)</span>

<span class="va">seurat_obj</span> <span class="op">&lt;-</span> <span class="fu">MetaspotsByGroups</span><span class="op">(</span>

<span class="va">seurat_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/MetaspotsByGroups.html">MetaspotsByGroups</a></span><span class="op">(</span>

  <span class="va">seurat_obj</span>,

  group.by <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"region"</span><span class="op">)</span>,

  ident.group <span class="op">=</span> <span class="st">"region"</span>,