createGiottoCosMxObject_all: Load and create a CosMx Giotto object from subcellular and...

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Load and create a CosMx Giotto object from subcellular and aggregate info

Description

Load and create a CosMx Giotto object from subcellular and aggregate info

Usage

createGiottoCosMxObject_all(
  dir_items,
  FOVs,
  remove_background_polygon = TRUE,
  background_algo = c("range"),
  remove_unvalid_polygons = TRUE,
  cores,
  verbose = TRUE,
  instructions = NULL
)

Arguments

dir_items	list of full directory paths from read_cosmx_folder
FOVs	field of views to load (only affects subcellular data and images)
remove_background_polygon	try to remove background polygon (default: FALSE)
background_algo	algorithm to remove background polygon
remove_unvalid_polygons	remove unvalid polygons (default: TRUE)
cores	how many cores or threads to use to read data if paths are provided
verbose	be verbose when building Giotto object
instructions	list of instructions or output result from createGiottoInstructions

Details

Both subcellular (subellular transcript detection information) and aggregate (aggregated detection count matrices by cell polygon from NanoString) data will be loaded in. The two will be separated into 'cell' and 'cell_agg' spatial units in order to denote the difference in origin of the two.

See Also

createGiottoCosMxObject createGiottoCosMxObject_aggregate createGiottoCosMxObject_subcellular

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.