neighbors/spatial_neighborhood_graph

Description

Calculates a spatial neighborhood graph based on the spatial coordinates.

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_obsm_spatial_coords: [ "spatial" ]  
coord_type: [ "generic" ]  
n_spatial_neighbors: [ 6 ]  
delaunay: [ false ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/neighbors/spatial_neighborhood_graph/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input H5MU file
--modality	string	Which modality from the input MuData file to process.
--input_obsm_spatial_coords	string	Key in adata.obsm where spatial coordinates are stored

Name

Type & Properties

--input

file

required

--modality

string

--input_obsm_spatial_coords

string

Spatial Neighbors Calculation

Name	Type & Properties	Description
--coord_type	string	Type of coordinate system. Valid options are: `grid` - grid coordinates. Only relevant for lattice-based layouts (e.g. Visium). Builds a graph assuming a regular grid topology, where neighbors aredefined by grid adjacency rather than distance. `generic` - Generic coordinates. Recommended for imaging-based data. This option is appropriate for irregularly spaced points, such as cell centroids or spot coordinates from imaging-based assays (e.g. Xenium, CosMx). Setting this option avoids grid-assumption artifacts and ensures each node has spatial neighbors as defined by distance.
--n_spatial_neighbors	integer	Depending on `--coord_type`: `grid` - number of neighboring tiles. `generic` - number of neighborhoods for non-grid data. Only used when `--delaunay False`.
--delaunay	boolean	Whether to use Delaunay triangulation to determine spatial neighborhood graph. Only used when `--coord_type generic`.

Name

Type & Properties

--coord_type

string

--n_spatial_neighbors

integer

--delaunay

boolean

Outputs

Name	Type & Properties	Description
--output	file required output	Output H5MU file path.
--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_compression

string