giotto-class: S4 giotto Class
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox
giotto-class R Documentation
S4 giotto Class
Description
Framework of giotto object to store and work with spatial expression data
Details
[expression] There are several ways to provide expression information:
[expression_feat] The different features or modalities such as rna, protein, metabolites, ...
that are provided in the expression slot.
Slots
expressionexpression information
expression_featavailable features (e.g. rna, protein, ...)
spatial_locsspatial location coordinates for cells/spots/grids
spatial_infoinformation about spatial units (Giotto spatVector)
cell_metadatametadata for cells
feat_metadatametadata for available features
feat_infoinformation about features (Giotto spatVector)
cell_IDunique cell IDs
feat_IDunique feature IDs for all features or modalities
spatial_networkspatial network in data.table/data.frame format
spatial_gridspatial grid in data.table/data.frame format
spatial_enrichmentslot to save spatial enrichment-like results
dimension_reductionslot to save dimension reduction coordinates
nn_networknearest neighbor network in igraph format
imagesslot to store giotto images
largeImagesslot to store giottoLargeImage objects
parametersslot to save parameters that have been used
instructionsslot for global function instructions
offset_fileoffset file used to stitch together image fields
OS_platformOperating System to run Giotto analysis on
join_infoinformation about joined Giotto objects
multiomicsmultiomics integration results
drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.
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| giotto-class | R Documentation |
S4 giotto Class
Description
Framework of giotto object to store and work with spatial expression data
Details
[expression] There are several ways to provide expression information:
[expression_feat] The different features or modalities such as rna, protein, metabolites, ... that are provided in the expression slot.
Slots
expressionexpression information
expression_featavailable features (e.g. rna, protein, ...)
spatial_locsspatial location coordinates for cells/spots/grids
spatial_infoinformation about spatial units (Giotto spatVector)
cell_metadatametadata for cells
feat_metadatametadata for available features
feat_infoinformation about features (Giotto spatVector)
cell_IDunique cell IDs
feat_IDunique feature IDs for all features or modalities
spatial_networkspatial network in data.table/data.frame format
spatial_gridspatial grid in data.table/data.frame format
spatial_enrichmentslot to save spatial enrichment-like results
dimension_reductionslot to save dimension reduction coordinates
nn_networknearest neighbor network in igraph format
imagesslot to store giotto images
largeImagesslot to store giottoLargeImage objects
parametersslot to save parameters that have been used
instructionsslot for global function instructions
offset_fileoffset file used to stitch together image fields
OS_platformOperating System to run Giotto analysis on
join_infoinformation about joined Giotto objects
multiomicsmultiomics integration results
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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