getSpatialEnrichment: Get spatial enrichment

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Get spatial enrichment

Description

Function to get a spatial enrichment data.table

Usage

getSpatialEnrichment(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  name = "DWLS",
  output = c("spatEnrObj", "data.table"),
  copy_obj = TRUE,
  set_defaults = TRUE
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
name	name of spatial enrichment results. Default "DWLS"
output	what format in which to get information (e.g. "data.table")
copy_obj	whether to deep copy/duplicate when getting the object (default = TRUE)
set_defaults	set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.

Value

data.table with fractions

See Also

Other spatial enrichment data accessor functions: get_spatial_enrichment(), setSpatialEnrichment(), set_spatial_enrichment()

Other functions to get data from giotto object: getDimReduction(), getExpression(), getFeatureInfo(), getGiottoImage(), getMultiomics(), getNearestNetwork(), getPolygonInfo(), getSpatialGrid(), getSpatialLocations(), getSpatialNetwork(), get_NearestNetwork(), get_dimReduction(), get_feature_info(), get_giottoImage(), get_multiomics(), get_polygon_info(), get_spatialGrid(), get_spatialNetwork(), get_spatial_enrichment(), get_spatial_locations()

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.