set_spatial_locations | R Documentation |
Function to set a spatial location slot
set_spatial_locations(
gobject,
spatlocs,
spat_unit = NULL,
spat_loc_name = "raw",
provenance = NULL,
verbose = TRUE,
set_defaults = TRUE,
initialize = FALSE
)
gobject |
giotto object |
spatlocs |
spatial locations (accepts either |
spat_unit |
spatial unit (e.g. "cell") |
spat_loc_name |
name of spatial locations, default "raw" |
provenance |
provenance information (optional) |
verbose |
be verbose |
set_defaults |
set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist. |
initialize |
(default = FALSE) whether to initialize the gobject before returning |
If a spatLocsObj
is provided to spatlocs
param then any
attached name and spat_unit info will be used for input to this function's
spat_loc_name
and spat_unit
params, BUT will be overridden by any
alternative specific inputs to those params.
ie: a spatLocsObj
with spat_unit slot == 'cell' will be automatically
nested by spat_unit 'cell' when using set_spatial_locations
as long as
param spat_unit = NULL
. BUT if param spat_unit = 'nucleus'
then
the spatLocsObj
will be nested by spat_unit 'nucleus' instead and
its spat_unit slot will be changed to 'nucleus'
giotto object
Other spatial location data accessor functions:
getSpatialLocations()
,
get_spatial_locations()
,
setSpatialLocations()
Other functions to set data in giotto object:
get_cell_id()
,
get_feat_id()
,
setCellMetadata()
,
setDimReduction()
,
setExpression()
,
setFeatureInfo()
,
setFeatureMetadata()
,
setGiottoImage()
,
setMultiomics()
,
setNearestNetwork()
,
setPolygonInfo()
,
setSpatialEnrichment()
,
setSpatialGrid()
,
setSpatialLocations()
,
setSpatialNetwork()
,
set_NearestNetwork()
,
set_cell_id()
,
set_cell_metadata()
,
set_dimReduction()
,
set_expression_values()
,
set_feat_id()
,
set_feature_info()
,
set_giottoImage()
,
set_multiomics()
,
set_polygon_info()
,
set_spatialGrid()
,
set_spatialNetwork()
,
set_spatial_enrichment()
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