dimred/lsi
Description
Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and singular values. Uses the implementation of scipy.
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. |
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. |
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. |
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 v3.0.2 \
-main-script target/nextflow/dimred/lsi/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
dimred/lsiopenpipeline v3.0.2
Uses
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