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.
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. |
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) |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output Seurat file |
--assay | string | Name of the assay to be created. |
--x_mapping | string | Name of the Seurat layer in which the AnnData .X matrix is stored. |
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" ]
x_mapping: [ "counts" ]
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/convert/from_h5mu_to_seurat_with_fov/main.nf \
-params-file params.yaml Relationships
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Current component
convert/from_h5mu_to_seurat_with_fovopenpipeline_spatial v0.7.0
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