S4 giotto Class

Giotto's core object that encapsulates all the components of a spatial-omic project and facilitates analyses.

Value

giotto object

Details

[initialize] The giotto class has a robust initialize() method that is automatically called upon setting data into the object, updates of the giottoInstructions, and loading of saved objects. It performs the following steps:

1. Update the object and subobjects for class definition changes if needed

2. Ensure a set of giottoInstructions are available, otherwise generate defaults

3. Ensure a giotto python environment is accessible when the options giotto.has_conda and giotto.use_conda are TRUE

4. Check the active spat_unit and feat_type

5. Ensure spatial/cell ID consistency and initialize the cell_ID and feat_ID slots for the active spat_unit and feat_type, as well as cell and feature metadata if they do not exist. Values for IDs and metadata are pulled from any existing data in spatial_info/feat_info or expression slots, with a preference for the latter.

6. Perform slot-specific and hierarchical checks that ensure dependent pieces of information are only added AFTER the data that they depend on and that existing information is consistent across slots.

7. Object validity checking

Slots

expression

expression information

expression_feat

The different features or modalities such as rna, protein, metabolites, ... that are provided in the expression slot.

spatial_locs

spatial location coordinates for cells/spots/grids

spatial_info

information about spatial units (Giotto spatVector)

cell_metadata

metadata for cells

feat_metadata

metadata for available features

feat_info

information about features (Giotto spatVector)

cell_ID

unique cell IDs

feat_ID

unique feature IDs for all features or modalities

spatial_network

spatial network in data.table/data.frame format

spatial_grid

spatial grid in data.table/data.frame format

spatial_enrichment

slot to save spatial enrichment-like results

dimension_reduction

slot to save dimension reduction coordinates

nn_network

nearest neighbor network in igraph format

images

slot to store giotto image objects

parameters

slot to save parameters that have been used

instructions

slot for global function instructions

offset_file

offset file used to stitch together image fields

versions

giotto object metadata and versioning info

join_info

information about joined Giotto objects

multiomics

multiomics integration results

h5_file

path to h5 file

Examples

giotto()
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"
#> An object of class giotto 
#> [SUBCELLULAR INFO]
#> [AGGREGATE INFO]
#> 
#> 
#> Use objHistory() to see steps and params used