Create Nanostring CosMx Giotto Object

Source: R/convenience_cosmx.R

Given the path to a CosMx experiment directory, creates a Giotto object.

createGiottoCosMxObject(
  cosmx_dir = NULL,
  data_to_use = c("all", "subcellular", "aggregate"),
  remove_background_polygon = TRUE,
  background_algo = c("range"),
  remove_unvalid_polygons = TRUE,
  FOVs = NULL,
  instructions = NULL,
  cores = determine_cores(),
  verbose = TRUE
)

Arguments

cosmx_dir

full path to the exported cosmx directory

data_to_use

which type(s) of expression data to build the gobject with Default is 'all' information available. 'subcellular' loads the transcript coordinates only. 'aggregate' loads the provided aggregated expression matrix.

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)

FOVs

field of views to load (only affects subcellular data and images)

instructions

list of instructions or output result from createGiottoInstructions

cores

how many cores or threads to use to read data if paths are provided

verbose

be verbose when building Giotto object

Value

a giotto object

Details

[Expected Directory] This function generates a giotto object when given a link to a cosmx output directory. It expects the following items within the directory where the bolded portions are what this function matches against:

  • CellComposite (folder of images)

  • CellLabels (folder of images)

  • CellOverlay (folder of images)

  • CompartmentLabels (folder of images)

  • experimentname_exprMat_file.csv (file)

  • experimentname_fov_positions_file.csv (file)

  • experimentname_metadata_file.csv (file)

  • experimentname_tx_file.csv (file)

[Workflows] Workflow to use is accessed through the data_to_use param

  • 'all' - loads and requires subcellular information from tx_file and fov_positions_file and also the existing aggregated information (expression, spatial locations, and metadata) from exprMat_file and metadata_file.

  • 'subcellular' - loads and requires subcellular information from tx_file and fov_positions_file only.

  • 'aggregate' - loads and requires the existing aggregate information (expression, spatial locations, and metadata) from exprMat_file and metadata_file.

[Images] Images in the default CellComposite, CellLabels, CompartmentLabels, and CellOverlay folders will be loaded as giotto largeImage objects in all workflows as long as they are available. Additionally, CellComposite images will be converted to giotto image objects, making plotting with these image objects more responsive when accessing them from a server. showGiottoImageNames can be used to see the available images.