added docstrings for modpres

export(ModuleExprScore)

export(ModuleFeaturePlot)

export(ModuleNetworkPlot)

export(ModulePreservation)

export(ModuleTraitCorrelation)

export(ModuleUMAPPlot)

export(MotifOverlapBarPlot)

export(OverlapModulesDEGs)

export(OverlapModulesMotifs)

export(PlotDendrogram)

export(PlotModulePreservation)

export(ProjectModules)

export(ROCCurves)

export(ResetModuleColors)

#'

#' Computes module preservation statistics in a query dataset for a given reference dataset

#'

#'

#' @param seurat_obj A Seurat object

#' @param seurat_ref A Seurat object serving as the reference for the module preservation analysis

#' @param name The name to give the module preservation analysis.

#' @param n_permutations Number of permutations for the module preservation test.

#' @param parallel logical determining whether to run preservation analysis in parallel

#' @param seed random seed for the permutation analysis.

#' @param return_raw if TRUE, returns the module preservation statistics, else returns seurat_obj with the stats added to the scWGCNA experiment.

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @param wgcna_name_ref The name of the scWGCNA experiment in the seurat_ref@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples

}

#' PlotModulePreservatgion

#'

#' Plotting function for Module Preservation statistics

#'

#' @param seurat_obj A Seurat object

#' @param name The name of the module preservation analysis to plot given in ModulePreservation

#' @param statistics Which module preservation statistics to plot? Choices are summary, all, or a custom list

#' @param plot_labels logical determining whether to plot the module labels

#' @param label_size the size of the module labels

#' @param mod_point_size the size of the points in each plot

#' @param wgcna_name The name of the scWGCNA experiment in the seurat_obj@misc slot

#' @keywords scRNA-seq

#' @export

#' @examples

#' PlotModulePreservation

PlotModulePreservation <- function(

  seurat_obj,

  name,

  desc: Functions for generating plots with scWGCNA

  contents:

  - '`ModuleFeaturePlot`'

- title: Module Preservation

  desc: Functions for performing module preservation analysis

  contents:

  - '`ModulePreservation`'

  - '`PlotModulePreservation`'

- title: Seurat wrappers

  desc: Wrapper functions to run Seurat commands on the metacell data

  contents:

  motif_analysis: motif_analysis.html

  network_visualizations: network_visualizations.html

  projecting_modules: projecting_modules.html

last_built: 2022-02-15T23:26Z

last_built: 2022-02-17T03:03Z

urls:

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

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