createGiottoObjectSubcellular: Create a giotto object from subcellular data
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

createGiottoObjectSubcellular

R Documentation

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(
  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
`largeImages_list_params`	image params when loading largeImages as list
`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)