Convert SpatialData to Giotto

Converts a saved SpatialData object into a Giotto object

Usage

spatialdataToGiotto(
  spatialdata_path = NULL,
  n_key_added = NULL,
  spatial_n_key_added = NULL,
  delaunay_spat_net = TRUE,
  spat_enrich_key_added = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  python_path = NULL,
  env_name = NULL
)

Arguments

spatialdata_path

path to SpatialData object

n_key_added

equivalent of "key_added" argument from scanpy.pp.neighbors(). If multiple spatial networks are in the anndata object, a list of key_added terms may be provided. If converting an anndata object from giottoToAnnData, the keys are saved in .uns['NN_keys'] and all keys are used in conversion unless specified in the function call. Cannot be "spatial". This becomes the name of the nearest network in the gobject.

spatial_n_key_added

equivalent of "key_added" argument from squidpy.gr.spatial_neighbors. If multiple spatial networks are in the anndata object, a list of key_added terms may be provided. If converting a SpatialData object from giottoToSpatialData, the keys are saved in .uns['SN_keys'] and all keys are used in conversion unless specified in the function call. Cannot be the same as n_key_added.

delaunay_spat_net

binary parameter for spatial network. If TRUE, the spatial network is a delaunay network.

spat_enrich_key_added

list of names of spatial enrichment annotations added to the SpatialData object. If converting an anndata object from giottoToAnnData and the original Giotto object had spatial enrichment annotations, the keys are saved in .uns['SE_keys'] and all keys are used in conversion unless specified in the function call.

spat_unit

desired spatial unit for conversion, default NULL

feat_type

desired feature type for conversion, default NULL

python_path

path to python executable within a conda/miniconda environment

env_name

name of environment containing python_path executable

Value

Giotto object

Details

Function in beta. Converts a structured SpatialData file into a Giotto object. The returned Giotto Object will take default insructions with the exception of the python path, which may be customized. See changeGiottoInstructions to modify instructions after creation.