createGiottoObjectSubcellular#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/giotto.R#L2272

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#

Argument

Description

gpolygons

giotto polygons

polygon_mask_list_params

list parameters for ``createGiottoPolygonsFromMask ` <#creategiottopolygonsfrommask>`__

polygon_dfr_list_params

list parameters for ``createGiottoPolygonsFromDfr ` <#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 `createGiottoInstructi ons <#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