Create Nanostring CosMx Giotto Object#
Last Updated: Oct 02, 2023
Given the path to a CosMx experiment directory, creates a Giotto object.
createGiottoCosMxObject( cosmx_dir = NULL, data_to_use = c("all", "subcellular", "aggregate"), FOVs = NULL, instructions = NULL, cores = NA, verbose = TRUE )
full path to the exported cosmx directory
which type(s) of expression data
to build the gobject with Default
field of views to load (only affects subcellular data and images)
list of instructions or output
how many cores or threads to use to read data if paths are provided
be verbose when building Giotto object
[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)
[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.
a giotto object