dimred/pca

Description

Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa11].

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: [ "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 v3.0.0 \  
  -main-script target/nextflow/dimred/pca/main.nf \  
  -params-file params.yaml

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.

Name

Type & Properties

--input

-i

file

required

--modality

string

--layer

string

--var_input

string

--output

-o

file

required

output

--obsm_output

string

--varm_output

string

--uns_output

string

--num_components

integer

--overwrite

boolean_true

--output_compression

string