User interface for the creation and validation of a new Region class object

Provides input type, name, and dimension checking for Region class objects

Usage

createRegionObject(
  Data,
  coordinates,
  id,
  cells = NULL,
  NormalizedData = NULL,
  ScaledData = NULL,
  bgData = NULL,
  representations = NULL,
  channelInfo = NULL,
  cellMetadata = NULL,
  features = NULL,
  featureInfo = NULL,
  neighborhoods = NULL,
  graphs = NULL,
  images = NULL,
  tiles = NULL,
  auto.spatial.representation = TRUE
)

Arguments

Data: Typically contains expression data, markers X cells
coordinates: Coordinates of cells in the currently-active segmentation
id: The name of the analysis
cells: A list of cells. List names correspond to Region ids
NormalizedData: Normalized Data
ScaledData: Scaled (centered and scaled) data
bgData: Any cell level information pertaining to background. Used for QC etc.
representations: Any representations of the data
channelInfo: Stores information about the microscope channel for each marker
cellMetadata: Stores cell information - clustering, etc.
features: Common features in the Analysis
featureInfo: Stores feature information - antibodies, barcodes, gene information, etc.
neighborhoods: A list of cell-cell interaction 'neighborhoods'
graphs: NN class objects for nearest neighbor representations
images: Stores links or actual image data. Note that this feature could explode the size of the SpatialMap
tiles: Stores information pertaining to any images that were stitched to form this Region. A mapping of cells to tiles
auto.spatial.representation: Whether the Create function automatically initializes a spatial Representation using cell coordinates.