GeneModuleOrder: #' GMOrder

In alexthiery/scHelper: R package containing helper functions for single cell analysis

#' GMOrder

Description

This function uses GeneModuleClassification to order GMs based on one or two cell metadata columns

Usage

GeneModuleOrder(
  seurat_obj,
  gene_modules,
  metadata_1 = NULL,
  order_1 = NULL,
  metadata_2 = NULL,
  order_2 = NULL,
  rename_modules = NULL,
  plot_path = "scHelper_log/GM_classification/"
)

Arguments

seurat_obj	Seurat object
gene_modules	List of gene modules generated by antler package
metadata_1	cell metadata column on which to order gms, first ordering
order_1	vector specifying order of values from metadata_1
metadata_2	cell metadata column on which to order gms, second ordering
order_2	vector specifying order of values from metadata_2
rename_modules	can be 'metadata_1' or 'metadata_2', will rename gms based on one of those classifications
plot_path	Directory to plot log files from GMClassification

Value

list of gms ordered by expression levels in cells across metadata1 and 2

alexthiery/scHelper documentation built on Aug. 26, 2023, 3:42 p.m.