neighbors/join_graphs
Description
Combine spatial and expression neighborhood graphs into a single graph for
use in downstream clustering or trajectory analysis.
The fusion is a linear combination of the expression connectivities
and spatial connectivities matrices, weighted by alpha.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input H5MU file with pre-computed expression and spatial neighborhood graphs. |
--modality | string | Modality from the input MuData file to process. |
--input_obsp_expression_graph | string | Key in `adata.obsp` containing the expression connectivity matrix. |
--input_obsp_spatial_graph | string | Key in `adata.obsp` containing the spatial connectivity matrix. |
Parameters
Name | Type & Properties | Description |
|---|---|---|
--alpha | double | Weight of the spatial graph in the connection fusion. A value of 0 results in the original expression graph; a value of 1 results in the spatial graph only. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output H5MU file path. |
--output_obsp_graph | string | Key under which to store the fused connectivity matrix in `adata.obsp`. |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
input_obsp_expression_graph: [ "connectivities" ]
input_obsp_spatial_graph: [ "spatial_connectivities" ]
alpha: [ 0.5 ]
output: "$id.$key.output.h5mu"
output_obsp_graph: [ "spatial_expression_connectivities" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \
-revision v0.7.0 \
-main-script target/nextflow/neighbors/join_graphs/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
neighbors/join_graphsopenpipeline_spatial v0.7.0
Uses
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