createGiottoObjectSubcellular

Create a giotto object from subcellular data

Description

Function to create a giotto object starting from subcellular polygon (e.g. cell) and points (e.g. transcripts) information

Usage

createGiottoObjectSubcellular(
  gpoints = NULL,
  gpolygons = NULL,
  polygon_mask_list_params = NA,
  polygon_dfr_list_params = NA,
  cell_metadata = NULL,
  feat_metadata = NULL,
  spatial_network = NULL,
  spatial_network_name = NULL,
  spatial_grid = NULL,
  spatial_grid_name = NULL,
  spatial_enrichment = NULL,
  spatial_enrichment_name = NULL,
  dimension_reduction = NULL,
  nn_network = NULL,
  images = NULL,
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

Arguments

Argument	Description
gpoints	giotto points
gpolygons	giotto polygons
polygon_mask_list_params	list parameters for ``createGiottoPolygonsFromMask` <#creategiottopolygonsfrommask>`_
polygon_dfr_list_params	list parameters for ``createGiottoPolygonsFromDfr` <#creategiottopolygonsfromdfr>`_
cell_metadata	cell annotation metadata
feat_metadata	feature annotation metadata for each unique feature
spatial_network	list of spatial network(s)
spatial_network_name	list of spatial network name(s)
spatial_grid	list of spatial grid(s)
spatial_grid_name	list of spatial grid name(s)
spatial_enrichment	list of spatial enrichment score(s) for each spatial region
spatial_enrichment_name	list of spatial enrichment name(s)
dimension_reduction	list of dimension reduction(s)
nn_network	list of nearest neighbor network(s)
images	list of images
instructions	list of instructions or output result from ``createGiottoInstructions` <#creategiottoinstructions>`_
cores	how many cores or threads to use to read data if paths are provided
verbose	be verbose when building Giotto object

Value

giotto object