Add new cascade analysis

Usage

add_cascade_analysis(
  obj_path,
  data_dir,
  project,
  analysis,
  cluster_markers = NULL,
  de_markers = NULL,
  conserved_markers = NULL,
  overwrite = FALSE,
  execute = FALSE
)

Arguments

obj_path: path to Seurat/anndata object
data_dir: output data directory. For convenience use the same data directory for all cascade projects.
project: project name. Creates a subfolder with this name inside data_dir if it doesn't exist.
analysis: analysis label. Creates a subfolder with this name inside data_dir/project
cluster_markers: (optional) path(s) to tab-delimited file(s) containing cluster markers. Output from Seurat's FindAllMarkers and scanpy's rank_genes_groups are supported.
de_markers: (optional) path(s) to tab-delimited file(s) containing differentially expressed markers from Seurat's FindMarkers or scanpy's rank_genes_groups.
conserved_markers: (optional) path(s) to tab-delimited file(s) containing conserved markers from Seurat's FindConservedMarkers function.
overwrite: boolean, if TRUE, existing analysis folder will be overwritten (default=FALSE)
execute: boolean, set this to TRUE to actually run the commands (default=FALSE)

Value

Invisibly returns NULL; called for the side effect of printing or executing setup commands.

Examples

if (FALSE) { # interactive()
local({
  data_dir <- tempfile("cascade-data-")
  dir.create(data_dir)

  obj_path <- tempfile("object-", fileext = ".rds")
  file.create(obj_path)

  on.exit(unlink(c(data_dir, obj_path), recursive = TRUE))

  add_cascade_analysis(
    obj_path = obj_path,
    data_dir = data_dir,
    project = "project1",
    analysis = "analysis1",
    execute = FALSE
  )
})
}