dimred/pca
Description
Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa11].
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input h5mu file |
--modality | string | Which modality from the input MuData file to process. |
--layer | string | Use specified layer for expression values instead of the .X object from the modality. |
--var_input | string | Column name in .var matrix that will be used to select which genes to run the PCA on. |
--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 resulting variance objects. |
--num_components | integer | Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. |
--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: [ "rna" ]
output: "$id.$key.output.h5mu"
obsm_output: [ "X_pca" ]
varm_output: [ "pca_loadings" ]
uns_output: [ "pca_variance" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.0 \
-main-script target/nextflow/dimred/pca/main.nf \
-params-file params.yaml Relationships
Used by
2 relationships
Current component
dimred/pcaopenpipeline v4.0.0
Uses
0 relationships
No component dependencies found.