Public
Edited
Jul 17, 2022
1 star
mermaid`
flowchart LR
classDef DT fill:#eef;
classDef CT fill:#fee;
classDef CV fill:#eff;
anndata.zarr-->anndataObsFeatureMatrix
anndata.zarr-->anndataObsSegmentations
anndata.zarr-->anndataObsEmbedding
subgraph Convenience file types
direction TB
subgraph anndata.zarr
direction RL
X
obsm/UMAP
obsm/spatial
end
end
subgraph File types and data types
anndataObsFeatureMatrix(anndataObsFeatureMatrix.zarr)
anndataObsSegmentations(anndataObsSegmentations.zarr)
anndataObsEmbedding(anndataObsEmbedding.zarr)
obsFeatureMatrix:::DT
obsSegmentations:::DT
obsEmbedding:::DT
anndataObsFeatureMatrix-->obsFeatureMatrix
anndataObsSegmentations-->obsSegmentations
anndataObsEmbedding-->obsEmbedding
end
obsFeatureMatrix--stores info about-->featureType
obsFeatureMatrix-->obsType
obsFeatureMatrix-->featureValueType
obsEmbedding-->obsType
obsEmbedding-->embeddingType
subgraph Coordination types
obsType---cell
featureType---peak
featureType---|has value|gene
embeddingType---UMAP
embeddingType---PCA
featureValueType---expression
obsType:::CT
featureType:::CT
featureValueType:::CT
embeddingType:::CT
cell(cell):::CV
gene(gene):::CV
peak:::CV
expression:::CV
UMAP(UMAP):::CV
PCA:::CV
end
cell===heatmapCTObsType
gene===|has matching value|heatmapCTFeatureType
cell===spatialCTObsType
cell===scatterplotCTObsType
UMAP===scatterplotCTEmbeddingType
expression===heatmapCTFeatureValueType
subgraph
direction TB
subgraph Heatmap view
direction LR
heatmapCTFeatureType---|uses for matching|heatmapTypeObsFeatureMatrix
heatmapCTFeatureValueType---heatmapTypeObsFeatureMatrix
heatmapCTObsType---heatmapTypeObsFeatureMatrix
heatmapTypeObsFeatureMatrix(obsFeatureMatrix):::DT
heatmapCTFeatureType(featureType: gene):::CV
heatmapCTFeatureValueType(featureValueType: expression):::CV
heatmapCTObsType(obsType: cell):::CV
end
subgraph Scatterplot view
direction LR
scatterplotCTObsType---scatterplotTypeObsEmbedding
scatterplotCTEmbeddingType---scatterplotTypeObsEmbedding
scatterplotTypeObsEmbedding(obsEmbedding):::DT
scatterplotCTObsType(obsType: cell):::CV
scatterplotCTEmbeddingType(embeddingType: UMAP):::CV
end
subgraph Spatial view
direction LR
spatialCTObsType---spatialTypeObsSegmentations
spatialTypeObsSegmentations(obsSegmentations):::DT
spatialCTObsType(obsType: cell):::CV
end
end
`
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