PlotDMEsVolcano

Plotting function for the results of FindDMEs and FindAllDMEs.

Usage

PlotDMEsVolcano(
  seurat_obj,
  DMEs,
  plot_labels = TRUE,
  mod_point_size = 4,
  label_size = 4,
  show_cutoff = TRUE,
  wgcna_name = NULL,
  xlim_range = NULL,
  ylim_range = NULL
)

Arguments

seurat_obj

A Seurat object containing the WGCNA analysis in the @misc slot.

DMEs

A dataframe output from FindDMEs or FindAllDMEs containing DME results.

plot_labels

Logical, determines whether to plot the module labels on the volcano plot. Default is TRUE.

mod_point_size

Numeric, the size of the points on the volcano plot. Default is 4.

label_size

Numeric, the size of the module labels on the plot. Default is 4.

show_cutoff

Logical, determines whether to plot the significance cutoff. Set this to FALSE if using facet_wrap. Default is TRUE.

wgcna_name

Character, the name of the hdWGCNA experiment in the seurat_obj@misc slot. Default is NULL, in which case it pulls the active WGCNA experiment from seurat_obj@misc$active_wgcna.

xlim_range

A numeric vector of length 2 specifying the x-axis limits for the log2 fold change. Default is NULL, which automatically calculates limits based on the data.

ylim_range

A numeric vector of length 2 specifying the y-axis limits for the -log10(p-value). Default is NULL, which automatically calculates limits based on the data.

Value

A ggplot object containing the volcano plot for the DME results.

Details

This function generates a volcano plot for differential module expression (DME) analysis results. It can handle both two-group comparisons (using the output of FindDMEs) and one-vs-all comparisons (using the output of FindAllDMEs).

Examples

# Example usage:
# Assuming `seurat_obj` is your Seurat object and `DMEs` is the output from FindDMEs
PlotDMEsVolcano(seurat_obj, DMEs, wgcna_name = "MG")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'na.omit': object 'DMEs' not found