convert/from_h5mu_to_seurat_with_fov

Description

Converts a single modality of an h5mu file into a Seurat object with a Field of View (FOV)
built from centroid coordinates of spatially-resolved single cells.

Type

r_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
obsm_centroid_coordinates: [ "spatial" ]  
output: "$id.$key.output.rds"  
assay: [ "RNA" ]  
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/convert/from_h5mu_to_seurat_with_fov/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string	Modality of the h5mu file to convert.
--obsm_centroid_coordinates	string	Key name of the .obsm slot in the input file that contains the spatial (centroid) coordinates.

Name

Type & Properties

--input

-i

file

required

--modality

string

--obsm_centroid_coordinates

string

Centroid arguments

Name	Type & Properties	Description
--centroid_nsides	integer	Number of sides of the polygon to be created around each centroid coordinate to represent the cell shape. If not provided, circles will be created.
--centroid_radius	double	Radius of the shape around each centroid coordinate to represent the cell shape. If not provided, Seurat computes a default based on the centroid coordinates.
--centroid_theta	double	Angle to adjust the shapes around each centroid when plotting. If not provided, no adjustment will be made (theta = 0)

Name

Type & Properties

--centroid_nsides

integer

--centroid_radius

double

--centroid_theta

double

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output Seurat file
--assay	string	Name of the assay to be created.

Name

Type & Properties

--output

-o

file

required

output

--assay

string