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.

Type

python_script

Links

Repository

Contributors

Launch

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 v0.5.0 \  
  -main-script target/nextflow/neighbors/join_graphs/main.nf \  
  -params-file params.yaml

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.

Name

Type & Properties

--input

file

required

--modality

string

--input_obsp_expression_graph

string

--input_obsp_spatial_graph

string

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.

Name

Type & Properties

--alpha

double

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.

Name

Type & Properties

--output

file

required

output

--output_obsp_graph

string

--output_compression

string