docstring for PlotKMEs/

Package: hdWGCNA

Title: WGCNA

Version: 0.1.1.9000

Version: 0.1.1.9001

Authors@R: c(

    person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),

           comment = c(ORCID = "0000-0002-7768-4856")),

export(OverlapModulesDEGs)

export(OverlapModulesMotifs)

export(PlotDendrogram)

export(PlotKMEs)

export(PlotModulePreservation)

export(PlotModuleTraitCorrelation)

export(PlotSoftPowers)

# hdWGCNA 0.1.1.9001 (2022-05-09)

## Added

- Wrote docstring for `PlotKMEs` so it would actually be included in the package.

## Changes

- None

# hdWGCNA 0.1.1.9000 (2022-05-05)

## Added

- `PlotKMEs` function to visualize the genes in a module ranked by kME.

    gene2 = as.character(edge_df[i,'Var2'])

    col1 <- selected_modules[selected_modules$gene_name == gene1, 'color']

    col2 <- selected_modules[selected_modules$gene_name == gene2, 'color']

    col2 <- selected_modules[sfelected_modules$gene_name == gene2, 'color']

    if(col1 == col2){

      col = col1

#' Plotting function for Module Preservation statistics

#'

#' @param seurat_obj A Seurat object

#' @param

#' @param

#' @param

#' @param

#' @param plot_labels logical determining whether to plot the module labels#' @param wgcna_name The name of the hdWGCNA experiment in the seurat_obj@misc slot

#' @param high_color color for positive correlation

#' @param mid_color color for zero correlation

#' @param low_color color for negative correlation

#' @param label logical determining whether to add p-val label in each cell of the heatmap

#' @param label_symbol show the labels as 'stars' or as 'numeric'

#' @param plot_max maximum value of correlation to show on the colorbar

#' @param text_size size of the labels

#' @param text_color color of the text labels

#' @param text_digits how many digits to show in the text labels

#' @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

}

#' PlotKMEs

#'

#' Plotting function to show genes by kME value in each module

#'

#' @param seurat_obj A Seurat object

#' @param n_hubs number of hub genes to display

#' @param text_size controls the size of the hub gene text

#' @param ncol number of columns to display individual plots

#' @param plot_widths the relative width between the kME rank plot and the hub gene text

#' @param wgcna_name the name of the WGCNA experiment in the seurat object

#' @keywords scRNA-seq

#' @export

#' @examples

#' PlotKMEs

PlotKMEs <- function(

  seurat_obj,

  n_hubs=10,

      </button>

      <span class="navbar-brand">

        <a class="navbar-link" href="https://smorabit.github.io/scWGCNA/index.html">hdWGCNA</a>

        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9000</span>

        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9001</span>

      </span>

    </div>