dimred/lsi

Description

Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and singular values. Uses the implementation of scipy.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "atac" ]  
num_components: [ 50 ]  
scale_embeddings: [ true ]  
output: "$id.$key.output.h5mu"  
obsm_output: [ "X_lsi" ]  
varm_output: [ "lsi" ]  
uns_output: [ "lsi" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/dimred/lsi/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Path to input h5mu file
--modality	string	On which modality to run LSI on.
--layer	string	Use specified layer for expression values. If not specified, uses adata.X.
--var_input	string	Column name in .var matrix that will be used to select which genes to run the LSI on. If not specified, uses all features.

Name

Type & Properties

--input

-i

file

required

--modality

string

--layer

string

--var_input

string

LSI options

Name	Type & Properties	Description
--num_components	integer	Number of components to compute.
--scale_embeddings	boolean	Scale embeddings to zero mean and unit variance.

Name

Type & Properties

--num_components

integer

--scale_embeddings

boolean

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.
--obsm_output	string	In which .obsm slot to store the resulting embedding.
--varm_output	string	In which .varm slot to store the resulting loadings matrix.
--uns_output	string	In which .uns slot to store the stdev.
--overwrite	boolean_true	Allow overwriting .obsm, .varm and .uns slots.
--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

-o

file

required

output

--obsm_output

string

--varm_output

string

--uns_output

string

--overwrite

boolean_true

--output_compression

string