Obtain overall percentage overlap between DEGs from bulk data (DE across all tissues) and various scRNA-seq datasets, across all common cell types

prop_bulk_DEGs_sc(
  bulkDE,
  bulk_cutoff = 0.9,
  pvalue = 0.05,
  sampled = c("individuals", "cells"),
  fontsize_axislabels = 12,
  fontsize_axisticks = 9,
  fontsize_title = 14,
  fontsize_legendlabels = 9,
  fontsize_legendtitle = 9,
  plot_title = "placeholder",
  output_path = getwd()
)

Arguments

bulkDE: DGE analysis output for a bulk RNA-seq dataset (e.g., LFSR.tsv): rows (rownames) should be the genes, columns should be tissues, and entries should be significance levels
bulk_cutoff: Numeric. Proportion (0–1) of bulk tissues in which a gene must be differentially expressed to be considered (e.g., 0.9 selects DEGs found in ≥90% of tissues).
pvalue: Numeric. P-value threshold for defining DEGs in the bulk dataset.
sampled: Specifies the unit of down-sampling. Can be either "individuals" or "cells", depending on whether the analysis downsamples across samples or cells.
fontsize_axislabels: font size for axis labels in plot
fontsize_axisticks: font size for axis tick labels in plot
fontsize_title: font size for plot title
fontsize_legendlabels: font size for legend labels in plot
fontsize_legendtitle: font size for legend title in plot
plot_title: plot title
output_path: A directory path where down-sampled outputs and diagnostic plots will be saved. Saves plot showing percentage DEGs from bulk data found in each scRNA-seq dataset, in the appropriate directory