Create differential expression analysis plots. Run by DGE_analysis()

Create differential expression analysis plots. Run by DGE_analysis()

plot_de_analysis(
  pb_dat,
  y,
  celltype_DEGs_dt,
  celltype_all_genes_dt,
  counts_celltypes,
  folder
)

Arguments

pb_dat

A list containing sumDat: matrix of the summed pseudobulk count values annot_pb: dataframe of the annotation data from the SCE rolled up based on the pseudobulk aggregation.

y

the column name in the SCE object for the return variable e.g. "diagnosis" - Case or disease. y can be discrete (logisitc regression) or continuous (linear regression)

celltype_DEGs_dt

data table containing the DEGs for each cell type with their differential expression data

celltype_all_genes_dt

data table containing the all genes for each cell type with their differential expression data

counts_celltypes

vector with the counts of cells after QC in each cell type

folder

the folder where the graphs from the differential expression analysis are saved. Default will create a folder in the current working directory "sc.cell.type.de.graphs". False will skip plotting. Creates and saves plot in relevant directory