createGiottoCosMxObject_subcellular: Load and create a CosMx Giotto object from subcellular info

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Load and create a CosMx Giotto object from subcellular info

Description

Load and create a CosMx Giotto object from subcellular info

Usage

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

Arguments

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

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