Create a giotto object from subcellular data#

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Last Updated: Mar 11, 2023

Description#

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

Usage#

createGiottoObjectSubcellular(
  gpolygons = NULL,
  polygon_mask_list_params = NULL,
  polygon_dfr_list_params = NULL,
  gpoints = NULL,
  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,
  largeImages = NULL,
  largeImages_list_params = NULL,
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

Arguments#

gpolygons

giotto polygons

polygon_mask_list_params

list parameters for createGiottoPolygonsFromMask

polygon_dfr_list_params

list parameters for createGiottoPolygonsFromDfr

gpoints

giotto points

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

largeImages

list of large 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

Details#

There are two different ways to create a Giotto Object with subcellular information: - Starting from polygons (spatial units e.g. cell) represented by a mask or dataframe file and giotto points (analyte coordinates e.g. transcripts) - Starting from polygons (spatial units e.g. cell) represented by a mask or dataframe file and raw intensity images (e.g. protein stains)

Value#

giotto object